4010
18.06.2020 09:15 UTC
EDAM http://edamontology.org/ "EDAM relations and concept properties"
EDAM_data http://edamontology.org/data_ "EDAM types of data"
EDAM_format http://edamontology.org/format_ "EDAM data formats"
EDAM_operation http://edamontology.org/operation_ "EDAM operations"
EDAM_topic http://edamontology.org/topic_ "EDAM topics"
EDAM editors: Jon Ison, Matúš Kalaš, Hervé Ménager, and Veit Schwämmle. Contributors: see http://edamontologydocs.readthedocs.io/en/latest/contributors.html. License: see http://edamontologydocs.readthedocs.io/en/latest/license.html.
EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.
Veit Schwämmle
Hervé Ménager
Jon Ison
Matúš Kalaš
application/rdf+xml
Bioinformatics operations, data types, formats, identifiers and topics
1.25
concept_properties "EDAM concept properties"
data "EDAM types of data"
edam "EDAM"
formats "EDAM data formats"
identifiers "EDAM types of identifiers"
operations "EDAM operations"
relations "EDAM relations"
topics "EDAM topics"
Jon Ison, Matúš Kalaš, Hervé Ménager
1.13
true
Publication reference
'Citation' concept property ('citation' metadata tag) contains a dereferenceable URI, preferrably including a DOI, pointing to a citeable publication of the given data format.
Publication
concept_properties
Citation
true
Version in which a concept was created.
concept_properties
Created in
true
A comment explaining why the comment should be or was deprecated, including name of person commenting (jison, mkalas etc.)
concept_properties
deprecation_comment
true
'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format.
Specification
concept_properties
Documentation
true
'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.
concept_properties
Separated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead.
Example
true
'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats.
concept_properties
N.B.: File extensions that are not correspondigly defined at http://filext.com are recorded in EDAM only if not in conflict with http://filext.com, and/or unique and usual within life-science computing.
Separated by bar ('|'), without a dot ('.') prefix, preferrably not all capital characters.
File extension
hasHumanReadableId
true
"Supported by the given data format" here means, that the given format enables representation of data that satisfies the information standard.
'Information standard' trailing modifier (qualifier, 'information_standard') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an information standard supported by the given data format.
Minimum information checklist
Minimum information standard
concept_properties
Information standard
true
When 'true', the concept has been proposed to be deprecated.
concept_properties
deprecation_candidate
true
When 'true', the concept has been proposed to be refactored.
concept_properties
refactor_candidate
true
When 'true', the concept has been proposed or is supported within Debian as a tag.
concept_properties
isdebtag
true
'Media type' trailing modifier (qualifier, 'media_type') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page specifying a media type of the given data format.
MIME type
concept_properties
Media type
true
Whether terms associated with this concept are recommended for use in annotation.
concept_properties
notRecommendedForAnnotation
true
Version in which a concept was made obsolete.
concept_properties
Obsolete since
true
EDAM concept URI of the erstwhile "parent" of a now deprecated concept.
concept_properties
Old parent
true
EDAM concept URI of an erstwhile related concept (by has_input, has_output, has_topic, is_format_of, etc.) of a now deprecated concept.
concept_properties
Old related
true
'Ontology used' concept property ('ontology_used' metadata tag) of format concepts links to a domain ontology that is used inside the given data format, or contains a note about ontology use within the format.
concept_properties
Ontology used
true
'Organisation' trailing modifier (qualifier, 'organisation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an organisation that developed, standardised, and maintains the given data format.
Organization
concept_properties
Organisation
true
A comment explaining the proposed refactoring, including name of person commenting (jison, mkalas etc.)
concept_properties
refactor_comment
true
'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.
concept_properties
Regular expression
true
'Repository' trailing modifier (qualifier, 'repository') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to the public source-code repository where the given data format is developed or maintained.
Public repository
Source-code repository
concept_properties
Repository
true
Name of thematic editor (http://biotools.readthedocs.io/en/latest/governance.html#registry-editors) responsible for this concept and its children.
concept_properties
thematic_editor
false
false
false
OBO_REL:is_a
'A has_format B' defines for the subject A, that it has the object B as its data format.
edam
relations
false
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'.
has format
"http://purl.obolibrary.org/obo/OBI_0000298"
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality"
false
false
false
OBO_REL:is_a
'A has_function B' defines for the subject A, that it has the object B as its function.
OBO_REL:bearer_of
edam
relations
true
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts.
has function
"http://purl.obolibrary.org/obo/OBI_0000306"
http://wsio.org/has_function
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality"
OBO_REL:bearer_of
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject.
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A has_identifier B' defines for the subject A, that it has the object B as its identifier.
edam
relations
false
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'.
has identifier
false
false
false
OBO_REL:is_a
'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument.
OBO_REL:has_participant
edam
relations
true
Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined.
has input
"http://purl.obolibrary.org/obo/OBI_0000293"
http://wsio.org/has_input
OBO_REL:has_participant
'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject.
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument.
OBO_REL:has_participant
edam
relations
true
Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined.
has output
"http://purl.obolibrary.org/obo/OBI_0000299"
http://wsio.org/has_output
OBO_REL:has_participant
'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it.
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).
edam
relations
true
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined.
has topic
"http://purl.obolibrary.org/obo/IAO_0000136"
"http://purl.obolibrary.org/obo/OBI_0000298"
http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A is_format_of B' defines for the subject A, that it is a data format of the object B.
OBO_REL:quality_of
edam
relations
false
Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined.
is format of
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in
OBO_REL:quality_of
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.
false
false
false
OBO_REL:is_a
'A is_function_of B' defines for the subject A, that it is a function of the object B.
OBO_REL:function_of
OBO_REL:inheres_in
edam
relations
true
Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used.
is function of
http://wsio.org/is_function_of
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in
OBO_REL:function_of
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object.
OBO_REL:inheres_in
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions.
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B.
edam
relations
false
Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined.
is identifier of
false
false
false
OBO_REL:is_a
'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B.
OBO_REL:participates_in
edam
relations
true
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'.
is input of
"http://purl.obolibrary.org/obo/OBI_0000295"
http://wsio.org/is_input_of
OBO_REL:participates_in
'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments.
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B.
OBO_REL:participates_in
edam
relations
true
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'.
is output of
"http://purl.obolibrary.org/obo/OBI_0000312"
http://wsio.org/is_output_of
OBO_REL:participates_in
'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it.
true
In very unusual cases.
false
false
false
OBO_REL:is_a
'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B).
OBO_REL:quality_of
edam
relations
true
Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'.
is topic of
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in
OBO_REL:quality_of
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.
true
In very unusual cases.
beta12orEarlier
beta12orEarlier
A type of computational resource used in bioinformatics.
Resource type
true
beta12orEarlier
true
Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.
Data record
Data set
Datum
Data
"http://purl.obolibrary.org/obo/IAO_0000027"
"http://purl.obolibrary.org/obo/IAO_0000030"
http://purl.org/biotop/biotop.owl#DigitalEntity
http://semanticscience.org/resource/SIO_000069
http://semanticscience.org/resource/SIO_000088
http://wsio.org/data_002
http://www.ifomis.org/bfo/1.1/snap#Continuant
http://www.onto-med.de/ontologies/gfo.owl#Perpetuant
Data record
EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information).
Data set
EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).
Datum
EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).
beta12orEarlier
beta12orEarlier
A bioinformatics package or tool, e.g. a standalone application or web service.
Tool
true
beta12orEarlier
beta12orEarlier
A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.
Database
true
beta12orEarlier
An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.
Ontology
beta12orEarlier
1.5
A directory on disk from which files are read.
Directory metadata
true
beta12orEarlier
beta12orEarlier
Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.
MeSH vocabulary
true
beta12orEarlier
beta12orEarlier
Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.
HGNC vocabulary
true
beta12orEarlier
beta12orEarlier
Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).
UMLS vocabulary
true
beta12orEarlier
true
A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).
ID
Identifier
"http://purl.org/dc/elements/1.1/identifier"
http://semanticscience.org/resource/SIO_000115
http://wsio.org/data_005
Almost exact but limited to identifying resources.
beta12orEarlier
beta12orEarlier
An entry (retrievable via URL) from a biological database.
Database entry
true
beta12orEarlier
Mass of a molecule.
Molecular mass
beta12orEarlier
PDBML:pdbx_formal_charge
Net charge of a molecule.
Molecular charge
beta12orEarlier
A specification of a chemical structure.
Chemical structure specification
Chemical formula
beta12orEarlier
A QSAR quantitative descriptor (name-value pair) of chemical structure.
QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.
QSAR descriptor
beta12orEarlier
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
1.23
A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.
Non-sequence characters may be used for example for gaps and translation stop.
Raw sequence
true
beta12orEarlier
SO:2000061
A molecular sequence and associated metadata.
Sequence record
http://purl.bioontology.org/ontology/MSH/D058977
beta12orEarlier
A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
Alignment reference
SO:0001260
An example is an alignment reference; one or a set of reference molecular sequences, structures, or profiles used for alignment of genomic, transcriptomic, or proteomic experimental data.
This concept may be used for arbitrary sequence sets and associated data arising from processing.
Sequence set
beta12orEarlier
1.5
A character used to replace (mask) other characters in a molecular sequence.
Sequence mask character
true
beta12orEarlier
1.5
A label (text token) describing the type of sequence masking to perform.
Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
Sequence mask type
true
beta12orEarlier
1.20
The strand of a DNA sequence (forward or reverse).
The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used.
DNA sense specification
true
beta12orEarlier
1.5
A specification of sequence length(s).
Sequence length specification
true
beta12orEarlier
1.5
Basic or general information concerning molecular sequences.
This is used for such things as a report including the sequence identifier, type and length.
Sequence metadata
true
beta12orEarlier
How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.
This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human).
Sequence feature source
beta12orEarlier
A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.
Database hits (sequence)
Sequence database hits
Sequence database search results
Sequence search hits
The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.
Sequence search results
beta12orEarlier
Report on the location of matches ("hits") between sequences, sequence profiles, motifs (conserved or functional patterns) and other types of sequence signatures.
Profile-profile alignment
Protein secondary database search results
Search results (protein secondary database)
Sequence motif hits
Sequence motif matches
Sequence profile alignment
Sequence profile hits
Sequence profile matches
Sequence-profile alignment
A "profile-profile alignment" is an alignment of two sequence profiles, each profile typically representing a sequence alignment.
A "sequence-profile alignment" is an alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).
This includes reports of hits from a search of a protein secondary or domain database. Data associated with the search or alignment might also be included, e.g. ranked list of best-scoring sequences, a graphical representation of scores etc.
Sequence signature matches
beta12orEarlier
beta12orEarlier
Data files used by motif or profile methods.
Sequence signature model
true
beta12orEarlier
Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.
This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on.
Sequence signature data
beta12orEarlier
1.5
Alignment of exact matches between subsequences (words) within two or more molecular sequences.
Sequence word alignment
Sequence alignment (words)
true
beta12orEarlier
A dotplot of sequence similarities identified from word-matching or character comparison.
Dotplot
beta12orEarlier
Alignment of multiple molecular sequences.
Multiple sequence aligment
msa
Sequence alignment
http://en.wikipedia.org/wiki/Sequence_alignment
http://purl.bioontology.org/ontology/MSH/D016415
http://semanticscience.org/resource/SIO_010066
beta12orEarlier
1.5
Some simple value controlling a sequence alignment (or similar 'match') operation.
Sequence alignment parameter
true
beta12orEarlier
A value representing molecular sequence similarity.
Sequence similarity score
beta12orEarlier
1.5
Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.
Sequence alignment metadata
true
beta12orEarlier
An informative report of molecular sequence alignment-derived data or metadata.
Sequence alignment metadata
Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score.
Sequence alignment report
beta12orEarlier
"Sequence-profile alignment" and "Profile-profile alignment" are synonymous with "Sequence signature matches" which was already stated as including matches (alignment) and other data.
A profile-profile alignment (each profile typically representing a sequence alignment).
Profile-profile alignment
true
beta12orEarlier
"Sequence-profile alignment" and "Profile-profile alignment" are synonymous with "Sequence signature matches" which was already stated as including matches (alignment) and other data.
1.24
Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).
Sequence-profile alignment
true
beta12orEarlier
Moby:phylogenetic_distance_matrix
A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.
Phylogenetic distance matrix
Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.
Sequence distance matrix
beta12orEarlier
Basic character data from which a phylogenetic tree may be generated.
As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments
Phylogenetic character data
http://www.evolutionaryontology.org/cdao.owl#Character
beta12orEarlier
Moby:Tree
Moby:myTree
Moby:phylogenetic_tree
The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.
Phylogeny
A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.
Phylogenetic tree
http://purl.bioontology.org/ontology/MSH/D010802
http://www.evolutionaryontology.org/cdao.owl#Tree
beta12orEarlier
Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.
Substitution matrix
The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).
Comparison matrix
beta12orEarlier
beta12orEarlier
Predicted or actual protein topology represented as a string of protein secondary structure elements.
The location and size of the secondary structure elements and intervening loop regions is usually indicated.
Protein topology
true
beta12orEarlier
1.8
Secondary structure (predicted or real) of a protein.
Protein features report (secondary structure)
true
beta12orEarlier
1.8
Super-secondary structure of protein sequence(s).
Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
Protein features report (super-secondary)
true
beta12orEarlier
true
Alignment of the (1D representations of) secondary structure of two or more proteins.
Secondary structure alignment (protein)
Protein secondary structure alignment
beta12orEarlier
beta12orEarlier
An informative report on protein secondary structure alignment-derived data or metadata.
Secondary structure alignment metadata (protein)
true
beta12orEarlier
Moby:RNAStructML
An informative report of secondary structure (predicted or real) of an RNA molecule.
Secondary structure (RNA)
This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.
RNA secondary structure
beta12orEarlier
true
Moby:RNAStructAlignmentML
Alignment of the (1D representations of) secondary structure of two or more RNA molecules.
Secondary structure alignment (RNA)
RNA secondary structure alignment
beta12orEarlier
beta12orEarlier
An informative report of RNA secondary structure alignment-derived data or metadata.
Secondary structure alignment metadata (RNA)
true
beta12orEarlier
3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.
Coordinate model
Structure data
The coordinate data may be predicted or real.
Structure
http://purl.bioontology.org/ontology/MSH/D015394
beta12orEarlier
beta12orEarlier
An entry from a molecular tertiary (3D) structure database.
Tertiary structure record
true
beta12orEarlier
1.8
Results (hits) from searching a database of tertiary structure.
Structure database search results
true
beta12orEarlier
Alignment (superimposition) of molecular tertiary (3D) structures.
A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.
Structure alignment
beta12orEarlier
An informative report of molecular tertiary structure alignment-derived data.
This is a broad data type and is used a placeholder for other, more specific types.
Structure alignment report
beta12orEarlier
A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.
Structure similarity score
beta12orEarlier
Some type of structural (3D) profile or template (representing a structure or structure alignment).
3D profile
Structural (3D) profile
Structural profile
beta12orEarlier
A 3D profile-3D profile alignment (each profile representing structures or a structure alignment).
Structural profile alignment
Structural (3D) profile alignment
beta12orEarlier
1.5
An alignment of a sequence to a 3D profile (representing structures or a structure alignment).
Sequence-structural profile alignment
Sequence-3D profile alignment
true
beta12orEarlier
Matrix of values used for scoring sequence-structure compatibility.
Protein sequence-structure scoring matrix
beta12orEarlier
An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).
Sequence-structure alignment
beta12orEarlier
1.4
An informative report about a specific amino acid.
Amino acid annotation
true
beta12orEarlier
1.4
An informative report about a specific peptide.
Peptide annotation
true
beta12orEarlier
An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.
Gene product annotation
Protein report
beta12orEarlier
A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.
Protein physicochemical property
Protein properties
Protein sequence statistics
This is a broad data type and is used a placeholder for other, more specific types. Data may be based on analysis of nucleic acid sequence or structural data, for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).
Protein property
beta12orEarlier
1.8
3D structural motifs in a protein.
Protein structural motifs and surfaces
true
beta12orEarlier
1.5
Data concerning the classification of the sequences and/or structures of protein structural domain(s).
Protein domain classification
true
beta12orEarlier
1.8
structural domains or 3D folds in a protein or polypeptide chain.
Protein features report (domains)
true
beta12orEarlier
1.4
An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.
Protein architecture report
true
beta12orEarlier
1.8
A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc.
Protein folding report
true
beta12orEarlier
beta13
Data on the effect of (typically point) mutation on protein folding, stability, structure and function.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein features (mutation)
true
beta12orEarlier
Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein interaction raw data
beta12orEarlier
Data concerning the interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc.
Protein interaction record
Protein interaction report
Protein report (interaction)
Protein-protein interaction data
Atom interaction data
Protein non-covalent interactions report
Residue interaction data
Protein interaction data
beta12orEarlier
Protein classification data
An informative report on a specific protein family or other classification or group of protein sequences or structures.
Protein family annotation
Protein family report
beta12orEarlier
The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.
Vmax
beta12orEarlier
Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.
Km
beta12orEarlier
1.4
An informative report about a specific nucleotide base.
Nucleotide base annotation
true
beta12orEarlier
Nucleic acid structural properties stiffness, curvature, twist/roll data or other conformational parameters or properties.
A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.
Nucleic acid physicochemical property
GC-content
Nucleic acid property (structural)
Nucleic acid structural property
This is a broad data type and is used a placeholder for other, more specific types.
Nucleic acid property
beta12orEarlier
Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.
Codon usage report
This is a broad data type and is used a placeholder for other, more specific types.
Codon usage data
beta12orEarlier
Moby:GeneInfo
Moby:gene
Moby_namespace:Human_Readable_Description
A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.
Gene and transcript structure (report)
Gene annotation
Gene features report
Gene function (report)
Gene structure (repot)
Nucleic acid features (gene and transcript structure)
This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).
Gene report
beta12orEarlier
beta12orEarlier
A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.
Gene classification
true
beta12orEarlier
1.8
stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.
DNA variation
true
beta12orEarlier
A human-readable collection of information about a specific chromosome.
This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.
Chromosome report
beta12orEarlier
A human-readable collection of information about the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.
Genotype/phenotype annotation
Genotype/phenotype report
beta12orEarlier
1.8
PCR experiments, e.g. quantitative real-time PCR.
PCR experiment report
true
beta12orEarlier
Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.
This is the raw data produced by a DNA sequencing machine.
Sequence trace
beta12orEarlier
An assembly of fragments of a (typically genomic) DNA sequence.
Contigs
SO:0000353
SO:0001248
Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.
Sequence assembly
http://en.wikipedia.org/wiki/Sequence_assembly
SO:0001248
Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'.
beta12orEarlier
Radiation hybrid scores (RH) scores for one or more markers.
Radiation Hybrid (RH) scores
Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.
RH scores
beta12orEarlier
A human-readable collection of information about the linkage of alleles.
Gene annotation (linkage)
Linkage disequilibrium (report)
This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
Genetic linkage report
beta12orEarlier
Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.
Gene expression pattern
Gene expression profile
beta12orEarlier
1.8
microarray experiments including conditions, protocol, sample:data relationships etc.
Microarray experiment report
true
beta12orEarlier
beta13
Data on oligonucleotide probes (typically for use with DNA microarrays).
Oligonucleotide probe data
true
beta12orEarlier
beta12orEarlier
Output from a serial analysis of gene expression (SAGE) experiment.
SAGE experimental data
true
beta12orEarlier
beta12orEarlier
Massively parallel signature sequencing (MPSS) data.
MPSS experimental data
true
beta12orEarlier
beta12orEarlier
Sequencing by synthesis (SBS) data.
SBS experimental data
true
beta12orEarlier
1.14
Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.
Sequence tag profile (with gene assignment)
true
beta12orEarlier
Protein X-ray crystallographic data
X-ray crystallography data.
Electron density map
beta12orEarlier
Nuclear magnetic resonance (NMR) raw data, typically for a protein.
Protein NMR data
Raw NMR data
beta12orEarlier
Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.
CD spectrum
Protein circular dichroism (CD) spectroscopic data
CD spectra
beta12orEarlier
Volume map data from electron microscopy.
3D volume map
EM volume map
Electron microscopy volume map
Volume map
beta12orEarlier
1.19
Annotation on a structural 3D model (volume map) from electron microscopy.
Electron microscopy model
true
beta12orEarlier
Two-dimensional gel electrophoresis image
2D PAGE image
beta12orEarlier
Spectra from mass spectrometry.
Mass spectrometry spectra
Mass spectrum
beta12orEarlier
A set of peptide masses (peptide mass fingerprint) from mass spectrometry.
Peak list
Protein fingerprint
Molecular weights standard fingerprint
A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides.
Peptide mass fingerprint
beta12orEarlier
Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer.
'Protein identification'
Peptide spectrum match
Peptide identification
beta12orEarlier
beta12orEarlier
An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.
Pathway or network annotation
true
beta12orEarlier
beta12orEarlier
A map (typically a diagram) of a biological pathway.
Biological pathway map
true
beta12orEarlier
1.5
A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.
Data resource definition
true
beta12orEarlier
Basic information, annotation or documentation concerning a workflow (but not the workflow itself).
Workflow metadata
beta12orEarlier
A biological model represented in mathematical terms.
Biological model
Mathematical model
beta12orEarlier
A value representing estimated statistical significance of some observed data; typically sequence database hits.
Statistical estimate score
beta12orEarlier
1.5
Resource definition for an EMBOSS database.
EMBOSS database resource definition
true
beta12orEarlier
1.5
Information on a version of software or data, for example name, version number and release date.
Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.
Version information
true
beta12orEarlier
A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.
The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.
Database cross-mapping
beta12orEarlier
An index of data of biological relevance.
Data index
beta12orEarlier
A human-readable collection of information concerning an analysis of an index of biological data.
Database index annotation
Data index report
beta12orEarlier
Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.
Database metadata
beta12orEarlier
Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.
Tool metadata
beta12orEarlier
1.5
Textual metadata on a submitted or completed job.
Job metadata
true
beta12orEarlier
Textual metadata on a software author or end-user, for example a person or other software.
User metadata
beta12orEarlier
A human-readable collection of information about a specific chemical compound.
Chemical compound annotation
Chemical structure report
Small molecule annotation
Small molecule report
beta12orEarlier
A human-readable collection of information about a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.
Cell line annotation
Organism strain data
Cell line report
beta12orEarlier
1.4
An informative report about a specific scent.
Scent annotation
true
beta12orEarlier
A term (name) from an ontology.
Ontology class name
Ontology terms
Ontology term
beta12orEarlier
Data concerning or derived from a concept from a biological ontology.
Ontology class metadata
Ontology term metadata
Ontology concept data
beta12orEarlier
Moby:BooleanQueryString
Moby:Global_Keyword
Moby:QueryString
Moby:Wildcard_Query
Keyword(s) or phrase(s) used (typically) for text-searching purposes.
Phrases
Term
Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.
Keyword
beta12orEarlier
Moby:GCP_SimpleCitation
Moby:Publication
Bibliographic data that uniquely identifies a scientific article, book or other published material.
Bibliographic reference
Reference
A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.
Citation
beta12orEarlier
A scientific text, typically a full text article from a scientific journal.
Article text
Scientific article
Article
beta12orEarlier
A human-readable collection of information resulting from text mining.
Text mining output
A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.
Text mining report
beta12orEarlier
beta12orEarlier
An identifier of a biological entity or phenomenon.
Entity identifier
true
beta12orEarlier
beta12orEarlier
An identifier of a data resource.
Data resource identifier
true
beta12orEarlier
true
An identifier that identifies a particular type of data.
Identifier (typed)
This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
Identifier (by type of data)
beta12orEarlier
true
An identifier of a bioinformatics tool, e.g. an application or web service.
Tool identifier
beta12orEarlier
beta12orEarlier
Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).
Discrete entity identifier
true
beta12orEarlier
beta12orEarlier
Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing).
Entity feature identifier
true
beta12orEarlier
beta12orEarlier
Name or other identifier of a collection of discrete biological entities.
Entity collection identifier
true
beta12orEarlier
beta12orEarlier
Name or other identifier of a physical, observable biological occurrence or event.
Phenomenon identifier
true
beta12orEarlier
true
Name or other identifier of a molecule.
Molecule identifier
beta12orEarlier
true
Identifier (e.g. character symbol) of a specific atom.
Atom identifier
Atom ID
beta12orEarlier
true
Name of a specific molecule.
Molecule name
beta12orEarlier
Protein|DNA|RNA
1.5
A label (text token) describing the type a molecule.
For example, 'Protein', 'DNA', 'RNA' etc.
Molecule type
true
beta12orEarlier
beta12orEarlier
Unique identifier of a chemical compound.
Chemical identifier
true
beta12orEarlier
Name of a chromosome.
Chromosome name
beta12orEarlier
true
Identifier of a peptide chain.
Peptide identifier
beta12orEarlier
true
Identifier of a protein.
Protein identifier
beta12orEarlier
Unique name of a chemical compound.
Chemical name
Compound name
beta12orEarlier
Unique registry number of a chemical compound.
Chemical registry number
beta12orEarlier
beta12orEarlier
Code word for a ligand, for example from a PDB file.
Ligand identifier
true
beta12orEarlier
true
Identifier of a drug.
Drug identifier
beta12orEarlier
true
Identifier of an amino acid.
Residue identifier
Amino acid identifier
beta12orEarlier
true
Name or other identifier of a nucleotide.
Nucleotide identifier
beta12orEarlier
true
Identifier of a monosaccharide.
Monosaccharide identifier
beta12orEarlier
Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.
ChEBI chemical name
This is the recommended chemical name for use for example in database annotation.
Chemical name (ChEBI)
beta12orEarlier
IUPAC recommended name of a chemical compound.
IUPAC chemical name
Chemical name (IUPAC)
beta12orEarlier
International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO).
INN chemical name
Chemical name (INN)
beta12orEarlier
Brand name of a chemical compound.
Brand chemical name
Chemical name (brand)
beta12orEarlier
Synonymous name of a chemical compound.
Synonymous chemical name
Chemical name (synonymous)
beta12orEarlier
CAS registry number of a chemical compound; a unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.
CAS chemical registry number
Chemical registry number (CAS)
CAS number
beta12orEarlier
Beilstein registry number of a chemical compound.
Beilstein chemical registry number
Chemical registry number (Beilstein)
beta12orEarlier
Gmelin registry number of a chemical compound.
Gmelin chemical registry number
Chemical registry number (Gmelin)
beta12orEarlier
3-letter code word for a ligand (HET group) from a PDB file, for example ATP.
Component identifier code
Short ligand name
HET group name
beta12orEarlier
String of one or more ASCII characters representing an amino acid.
Amino acid name
beta12orEarlier
String of one or more ASCII characters representing a nucleotide.
Nucleotide code
beta12orEarlier
PDBML:pdbx_PDB_strand_id
WHATIF: chain
Identifier of a polypeptide chain from a protein.
Chain identifier
PDB chain identifier
PDB strand id
Polypeptide chain identifier
Protein chain identifier
This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA
Polypeptide chain ID
beta12orEarlier
Name of a protein.
Protein name
beta12orEarlier
Name or other identifier of an enzyme or record from a database of enzymes.
Enzyme identifier
beta12orEarlier
[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+
Moby:Annotated_EC_Number
Moby:EC_Number
An Enzyme Commission (EC) number of an enzyme.
EC
EC code
Enzyme Commission number
EC number
beta12orEarlier
Name of an enzyme.
Enzyme name
beta12orEarlier
Name of a restriction enzyme.
Restriction enzyme name
beta12orEarlier
1.5
A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.
Sequence position specification
true
beta12orEarlier
A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.
Sequence feature ID
beta12orEarlier
PDBML:_atom_site.id
WHATIF: PDBx_atom_site
WHATIF: number
A position of one or more points (base or residue) in a sequence, or part of such a specification.
SO:0000735
Sequence position
beta12orEarlier
Specification of range(s) of sequence positions.
Sequence range
beta12orEarlier
beta12orEarlier
Name or other identifier of an nucleic acid feature.
Nucleic acid feature identifier
true
beta12orEarlier
beta12orEarlier
Name or other identifier of a protein feature.
Protein feature identifier
true
beta12orEarlier
The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key.
Sequence feature method
Sequence feature type
A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.
Sequence feature key
beta12orEarlier
Typically one of the EMBL or Swiss-Prot feature qualifiers.
Feature qualifiers hold information about a feature beyond that provided by the feature key and location.
Sequence feature qualifier
beta12orEarlier
A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label.
Sequence feature name
A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature.
Sequence feature label
beta12orEarlier
The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.
UFO
EMBOSS Uniform Feature Object
beta12orEarlier
beta12orEarlier
String of one or more ASCII characters representing a codon.
Codon name
true
beta12orEarlier
true
Moby:GeneAccessionList
An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.
Gene identifier
beta12orEarlier
Moby_namespace:Global_GeneCommonName
Moby_namespace:Global_GeneSymbol
The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.
Gene symbol
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs:LocusID
http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene
An NCBI unique identifier of a gene.
Entrez gene ID
Gene identifier (Entrez)
Gene identifier (NCBI)
NCBI gene ID
NCBI geneid
Gene ID (NCBI)
beta12orEarlier
beta12orEarlier
An NCBI RefSeq unique identifier of a gene.
Gene identifier (NCBI RefSeq)
true
beta12orEarlier
beta12orEarlier
An NCBI UniGene unique identifier of a gene.
Gene identifier (NCBI UniGene)
true
beta12orEarlier
beta12orEarlier
[0-9]+
An Entrez unique identifier of a gene.
Gene identifier (Entrez)
true
beta12orEarlier
Identifier of a gene or feature from the CGD database.
CGD ID
Gene ID (CGD)
beta12orEarlier
Identifier of a gene from DictyBase.
Gene ID (DictyBase)
beta12orEarlier
Unique identifier for a gene (or other feature) from the Ensembl database.
Gene ID (Ensembl)
Ensembl gene ID
beta12orEarlier
S[0-9]+
Identifier of an entry from the SGD database.
SGD identifier
Gene ID (SGD)
beta12orEarlier
[a-zA-Z_0-9\.-]*
Moby_namespace:GeneDB
Identifier of a gene from the GeneDB database.
GeneDB identifier
Gene ID (GeneDB)
beta12orEarlier
Identifier of an entry from the TIGR database.
TIGR identifier
beta12orEarlier
Gene:[0-9]{7}
Identifier of an gene from the TAIR database.
TAIR accession (gene)
beta12orEarlier
true
Identifier of a protein structural domain.
This is typically a character or string concatenated with a PDB identifier and a chain identifier.
Protein domain ID
beta12orEarlier
Identifier of a protein domain (or other node) from the SCOP database.
SCOP domain identifier
beta12orEarlier
1nr3A00
Identifier of a protein domain from CATH.
CATH domain identifier
CATH domain ID
beta12orEarlier
A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.
An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.
SCOP concise classification string (sccs)
beta12orEarlier
33229
Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.
SCOP unique identifier
sunid
A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.
SCOP sunid
beta12orEarlier
3.30.1190.10.1.1.1.1.1
A code number identifying a node from the CATH database.
CATH code
CATH node identifier
CATH node ID
beta12orEarlier
The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).
Kingdom name
beta12orEarlier
The name of a species (typically a taxonomic group) of organism.
Organism species
Species name
beta12orEarlier
The name of a strain of an organism variant, typically a plant, virus or bacterium.
Strain name
beta12orEarlier
true
A string of characters that name or otherwise identify a resource on the Internet.
URIs
URI
beta12orEarlier
true
An identifier of a biological or bioinformatics database.
Database identifier
Database ID
beta12orEarlier
The name of a directory.
Directory name
beta12orEarlier
The name (or part of a name) of a file (of any type).
File name
beta12orEarlier
Name of an ontology of biological or bioinformatics concepts and relations.
Ontology name
beta12orEarlier
Moby:Link
Moby:URL
A Uniform Resource Locator (URL).
URL
beta12orEarlier
A Uniform Resource Name (URN).
URN
beta12orEarlier
A Life Science Identifier (LSID) - a unique identifier of some data.
Life Science Identifier
LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
LSID
beta12orEarlier
The name of a biological or bioinformatics database.
Database name
beta12orEarlier
beta13
The name of a molecular sequence database.
Sequence database name
true
beta12orEarlier
The name of a file (of any type) with restricted possible values.
Enumerated file name
beta12orEarlier
The extension of a file name.
A file extension is the characters appearing after the final '.' in the file name.
File name extension
beta12orEarlier
The base name of a file.
A file base name is the file name stripped of its directory specification and extension.
File base name
beta12orEarlier
Name of a QSAR descriptor.
QSAR descriptor name
beta12orEarlier
beta12orEarlier
An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.
This concept is required for completeness. It should never have child concepts.
Database entry identifier
true
beta12orEarlier
true
An identifier of molecular sequence(s) or entries from a molecular sequence database.
Sequence identifier
beta12orEarlier
true
An identifier of a set of molecular sequence(s).
Sequence set ID
beta12orEarlier
beta12orEarlier
Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns.
Sequence signature identifier
true
beta12orEarlier
true
Identifier of a molecular sequence alignment, for example a record from an alignment database.
Sequence alignment ID
beta12orEarlier
beta12orEarlier
Identifier of a phylogenetic distance matrix.
Phylogenetic distance matrix identifier
true
beta12orEarlier
true
Identifier of a phylogenetic tree for example from a phylogenetic tree database.
Phylogenetic tree ID
beta12orEarlier
true
An identifier of a comparison matrix.
Substitution matrix identifier
Comparison matrix identifier
beta12orEarlier
true
A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.
Structure ID
beta12orEarlier
true
Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment).
Structural profile identifier
Structural (3D) profile ID
beta12orEarlier
true
Identifier of an entry from a database of tertiary structure alignments.
Structure alignment ID
beta12orEarlier
true
Identifier of an index of amino acid physicochemical and biochemical property data.
Amino acid index ID
beta12orEarlier
true
Molecular interaction ID
Identifier of a report of protein interactions from a protein interaction database (typically).
Protein interaction ID
beta12orEarlier
true
Identifier of a protein family.
Protein secondary database record identifier
Protein family identifier
beta12orEarlier
Unique name of a codon usage table.
Codon usage table name
beta12orEarlier
true
Identifier of a transcription factor (or a TF binding site).
Transcription factor identifier
beta12orEarlier
true
Identifier of an entry from a database of microarray data.
Experiment annotation ID
beta12orEarlier
true
Identifier of an entry from a database of electron microscopy data.
Electron microscopy model ID
beta12orEarlier
true
Accession of a report of gene expression (e.g. a gene expression profile) from a database.
Gene expression profile identifier
Gene expression report ID
beta12orEarlier
true
Identifier of an entry from a database of genotypes and phenotypes.
Genotype and phenotype annotation ID
beta12orEarlier
true
Identifier of an entry from a database of biological pathways or networks.
Pathway or network identifier
beta12orEarlier
true
Identifier of a biological or biomedical workflow, typically from a database of workflows.
Workflow ID
beta12orEarlier
true
Identifier of a data type definition from some provider.
Data resource definition identifier
Data resource definition ID
beta12orEarlier
true
Identifier of a mathematical model, typically an entry from a database.
Biological model identifier
Biological model ID
beta12orEarlier
true
Identifier of an entry from a database of chemicals.
Chemical compound identifier
Compound ID
Small molecule identifier
Compound identifier
beta12orEarlier
A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.
Ontology concept ID
beta12orEarlier
true
Unique identifier of a scientific article.
Article identifier
Article ID
beta12orEarlier
FB[a-zA-Z_0-9]{2}[0-9]{7}
Identifier of an object from the FlyBase database.
FlyBase ID
beta12orEarlier
Name of an object from the WormBase database, usually a human-readable name.
WormBase name
beta12orEarlier
Class of an object from the WormBase database.
A WormBase class describes the type of object such as 'sequence' or 'protein'.
WormBase class
beta12orEarlier
true
A persistent, unique identifier of a molecular sequence database entry.
Sequence accession number
Sequence accession
beta12orEarlier
1.5
A label (text token) describing a type of molecular sequence.
Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
Sequence type
true
beta12orEarlier
The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.
EMBOSS USA
EMBOSS Uniform Sequence Address
beta12orEarlier
true
Accession number of a protein sequence database entry.
Protein sequence accession number
Sequence accession (protein)
beta12orEarlier
true
Accession number of a nucleotide sequence database entry.
Nucleotide sequence accession number
Sequence accession (nucleic acid)
beta12orEarlier
(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+
Accession number of a RefSeq database entry.
RefSeq ID
RefSeq accession
beta12orEarlier
Q7M1G0|P43353-2|P01012.107
1.0
[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+
Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.
UniProt accession (extended)
true
beta12orEarlier
An identifier of PIR sequence database entry.
PIR ID
PIR accession number
PIR identifier
beta12orEarlier
1.2
Identifier of a TREMBL sequence database entry.
TREMBL accession
true
beta12orEarlier
Primary identifier of a Gramene database entry.
Gramene primary ID
Gramene primary identifier
beta12orEarlier
Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.
EMBL/GenBank/DDBJ ID
beta12orEarlier
A unique identifier of an entry (gene cluster) from the NCBI UniGene database.
UniGene ID
UniGene cluster ID
UniGene identifier
Sequence cluster ID (UniGene)
beta12orEarlier
Identifier of a dbEST database entry.
dbEST ID
dbEST accession
beta12orEarlier
Identifier of a dbSNP database entry.
dbSNP identifier
dbSNP ID
beta12orEarlier
beta12orEarlier
The EMBOSS type of a molecular sequence.
See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.
EMBOSS sequence type
true
beta12orEarlier
1.5
List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).
EMBOSS listfile
true
beta12orEarlier
true
An identifier of a cluster of molecular sequence(s).
Sequence cluster ID
beta12orEarlier
Unique identifier of an entry from the COG database.
COG ID
Sequence cluster ID (COG)
beta12orEarlier
true
Identifier of a sequence motif, for example an entry from a motif database.
Sequence motif identifier
beta12orEarlier
true
Identifier of a sequence profile.
A sequence profile typically represents a sequence alignment.
Sequence profile ID
beta12orEarlier
Identifier of an entry from the ELMdb database of protein functional sites.
ELM ID
beta12orEarlier
PS[0-9]{5}
Accession number of an entry from the Prosite database.
Prosite ID
Prosite accession number
beta12orEarlier
Unique identifier or name of a HMMER hidden Markov model.
HMMER hidden Markov model ID
beta12orEarlier
Unique identifier or name of a profile from the JASPAR database.
JASPAR profile ID
beta12orEarlier
1.5
A label (text token) describing the type of a sequence alignment.
Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.
Sequence alignment type
true
beta12orEarlier
beta12orEarlier
The type of a BLAST sequence alignment.
BLAST sequence alignment type
true
beta12orEarlier
nj|upgmp
1.5
A label (text token) describing the type of a phylogenetic tree.
For example 'nj', 'upgmp' etc.
Phylogenetic tree type
true
beta12orEarlier
Accession number of an entry from the TreeBASE database.
TreeBASE study accession number
beta12orEarlier
Accession number of an entry from the TreeFam database.
TreeFam accession number
beta12orEarlier
blosum|pam|gonnet|id
1.5
A label (text token) describing the type of a comparison matrix.
For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used.
Comparison matrix type
true
beta12orEarlier
Unique name or identifier of a comparison matrix.
Substitution matrix name
See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.
Comparison matrix name
beta12orEarlier
[0-9][a-zA-Z_0-9]{3}
An identifier of an entry from the PDB database.
PDB identifier
PDBID
A PDB identification code which consists of 4 characters, the first of which is a digit in the range 0 - 9; the remaining 3 are alpha-numeric, and letters are upper case only. (source: https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1996.pdf)
PDB ID
beta12orEarlier
Identifier of an entry from the AAindex database.
AAindex ID
beta12orEarlier
Accession number of an entry from the BIND database.
BIND accession number
beta12orEarlier
EBI\-[0-9]+
Accession number of an entry from the IntAct database.
IntAct accession number
beta12orEarlier
Name of a protein family.
Protein family name
beta12orEarlier
Name of an InterPro entry, usually indicating the type of protein matches for that entry.
InterPro entry name
beta12orEarlier
IPR015590
IPR[0-9]{6}
Primary accession number of an InterPro entry.
InterPro primary accession
InterPro primary accession number
Every InterPro entry has a unique accession number to provide a persistent citation of database records.
InterPro accession
beta12orEarlier
Secondary accession number of an InterPro entry.
InterPro secondary accession number
InterPro secondary accession
beta12orEarlier
Unique identifier of an entry from the Gene3D database.
Gene3D ID
beta12orEarlier
PIRSF[0-9]{6}
Unique identifier of an entry from the PIRSF database.
PIRSF ID
beta12orEarlier
PR[0-9]{5}
The unique identifier of an entry in the PRINTS database.
PRINTS code
beta12orEarlier
PF[0-9]{5}
Accession number of a Pfam entry.
Pfam accession number
beta12orEarlier
SM[0-9]{5}
Accession number of an entry from the SMART database.
SMART accession number
beta12orEarlier
Unique identifier (number) of a hidden Markov model from the Superfamily database.
Superfamily hidden Markov model number
beta12orEarlier
Accession number of an entry (family) from the TIGRFam database.
TIGRFam accession number
TIGRFam ID
beta12orEarlier
PD[0-9]+
A ProDom domain family accession number.
ProDom is a protein domain family database.
ProDom accession number
beta12orEarlier
Identifier of an entry from the TRANSFAC database.
TRANSFAC accession number
beta12orEarlier
[AEP]-[a-zA-Z_0-9]{4}-[0-9]+
Accession number of an entry from the ArrayExpress database.
ArrayExpress experiment ID
ArrayExpress accession number
beta12orEarlier
[0-9]+
PRIDE experiment accession number.
PRIDE experiment accession number
beta12orEarlier
Identifier of an entry from the EMDB electron microscopy database.
EMDB ID
beta12orEarlier
o^GDS[0-9]+
Accession number of an entry from the GEO database.
GEO accession number
beta12orEarlier
Identifier of an entry from the GermOnline database.
GermOnline ID
beta12orEarlier
Identifier of an entry from the EMAGE database.
EMAGE ID
beta12orEarlier
true
Accession number of an entry from a database of disease.
Disease ID
beta12orEarlier
Identifier of an entry from the HGVbase database.
HGVbase ID
beta12orEarlier
beta12orEarlier
Identifier of an entry from the HIVDB database.
HIVDB identifier
true
beta12orEarlier
[*#+%^]?[0-9]{6}
Identifier of an entry from the OMIM database.
OMIM ID
beta12orEarlier
Unique identifier of an object from one of the KEGG databases (excluding the GENES division).
KEGG object identifier
beta12orEarlier
REACT_[0-9]+(\.[0-9]+)?
Identifier of an entry from the Reactome database.
Reactome ID
Pathway ID (reactome)
beta12orEarlier
beta12orEarlier
Identifier of an entry from the aMAZE database.
aMAZE ID
Pathway ID (aMAZE)
true
beta12orEarlier
Identifier of an pathway from the BioCyc biological pathways database.
BioCyc pathway ID
Pathway ID (BioCyc)
beta12orEarlier
Identifier of an entry from the INOH database.
INOH identifier
Pathway ID (INOH)
beta12orEarlier
Identifier of an entry from the PATIKA database.
PATIKA ID
Pathway ID (PATIKA)
beta12orEarlier
Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.
CPDB ID
This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.
Pathway ID (CPDB)
beta12orEarlier
PTHR[0-9]{5}
Identifier of a biological pathway from the Panther Pathways database.
Panther Pathways ID
Pathway ID (Panther)
beta12orEarlier
MIR:00100005
MIR:[0-9]{8}
Unique identifier of a MIRIAM data resource.
This is the identifier used internally by MIRIAM for a data type.
MIRIAM identifier
beta12orEarlier
The name of a data type from the MIRIAM database.
MIRIAM data type name
beta12orEarlier
urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202
The URI (URL or URN) of a data entity from the MIRIAM database.
identifiers.org synonym
A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.
MIRIAM URI
beta12orEarlier
UniProt|Enzyme Nomenclature
The primary name of a data type from the MIRIAM database.
The primary name of a MIRIAM data type is taken from a controlled vocabulary.
MIRIAM data type primary name
UniProt|Enzyme Nomenclature
A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'.
beta12orEarlier
A synonymous name of a data type from the MIRIAM database.
A synonymous name for a MIRIAM data type taken from a controlled vocabulary.
MIRIAM data type synonymous name
beta12orEarlier
Unique identifier of a Taverna workflow.
Taverna workflow ID
beta12orEarlier
Name of a biological (mathematical) model.
Biological model name
beta12orEarlier
(BIOMD|MODEL)[0-9]{10}
Unique identifier of an entry from the BioModel database.
BioModel ID
beta12orEarlier
[0-9]+
Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.
PubChem compound accession identifier
PubChem CID
beta12orEarlier
[0-9]+
Identifier of an entry from the ChemSpider database.
ChemSpider ID
beta12orEarlier
CHEBI:[0-9]+
Identifier of an entry from the ChEBI database.
ChEBI IDs
ChEBI identifier
ChEBI ID
beta12orEarlier
An identifier of a concept from the BioPax ontology.
BioPax concept ID
beta12orEarlier
[0-9]{7}|GO:[0-9]{7}
An identifier of a concept from The Gene Ontology.
GO concept identifier
GO concept ID
beta12orEarlier
An identifier of a concept from the MeSH vocabulary.
MeSH concept ID
beta12orEarlier
An identifier of a concept from the HGNC controlled vocabulary.
HGNC concept ID
beta12orEarlier
9662|3483|182682
[1-9][0-9]{0,8}
A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.
NCBI tax ID
NCBI taxonomy identifier
NCBI taxonomy ID
beta12orEarlier
An identifier of a concept from the Plant Ontology (PO).
Plant Ontology concept ID
beta12orEarlier
An identifier of a concept from the UMLS vocabulary.
UMLS concept ID
beta12orEarlier
FMA:[0-9]+
An identifier of a concept from Foundational Model of Anatomy.
Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
FMA concept ID
beta12orEarlier
An identifier of a concept from the EMAP mouse ontology.
EMAP concept ID
beta12orEarlier
An identifier of a concept from the ChEBI ontology.
ChEBI concept ID
beta12orEarlier
An identifier of a concept from the MGED ontology.
MGED concept ID
beta12orEarlier
An identifier of a concept from the myGrid ontology.
The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
myGrid concept ID
beta12orEarlier
4963447
[1-9][0-9]{0,8}
PubMed unique identifier of an article.
PMID
PubMed ID
beta12orEarlier
(doi\:)?[0-9]{2}\.[0-9]{4}/.*
Digital Object Identifier (DOI) of a published article.
Digital Object Identifier
DOI
beta12orEarlier
Medline UI (unique identifier) of an article.
Medline unique identifier
The use of Medline UI has been replaced by the PubMed unique identifier.
Medline UI
beta12orEarlier
The name of a computer package, application, method or function.
Tool name
beta12orEarlier
The unique name of a signature (sequence classifier) method.
Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.
Tool name (signature)
beta12orEarlier
The name of a BLAST tool.
BLAST name
This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'.
Tool name (BLAST)
beta12orEarlier
The name of a FASTA tool.
This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'.
Tool name (FASTA)
beta12orEarlier
The name of an EMBOSS application.
Tool name (EMBOSS)
beta12orEarlier
The name of an EMBASSY package.
Tool name (EMBASSY package)
beta12orEarlier
A QSAR constitutional descriptor.
QSAR constitutional descriptor
QSAR descriptor (constitutional)
beta12orEarlier
A QSAR electronic descriptor.
QSAR electronic descriptor
QSAR descriptor (electronic)
beta12orEarlier
A QSAR geometrical descriptor.
QSAR geometrical descriptor
QSAR descriptor (geometrical)
beta12orEarlier
A QSAR topological descriptor.
QSAR topological descriptor
QSAR descriptor (topological)
beta12orEarlier
A QSAR molecular descriptor.
QSAR molecular descriptor
QSAR descriptor (molecular)
beta12orEarlier
Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
Sequence set (protein)
beta12orEarlier
Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
Sequence set (nucleic acid)
beta12orEarlier
A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.
The cluster might include sequences identifiers, short descriptions, alignment and summary information.
Sequence cluster
beta12orEarlier
beta12orEarlier
A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.
A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'.
Psiblast checkpoint file
true
beta12orEarlier
beta12orEarlier
Sequences generated by HMMER package in FASTA-style format.
HMMER synthetic sequences set
true
beta12orEarlier
A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.
Proteolytic digest
beta12orEarlier
SO:0000412
Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.
Restriction digest
beta12orEarlier
Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.
PCR primers
beta12orEarlier
beta12orEarlier
File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.
vectorstrip cloning vector definition file
true
beta12orEarlier
beta12orEarlier
A library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.
Primer3 internal oligo mishybridizing library
true
beta12orEarlier
beta12orEarlier
A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format.
Primer3 mispriming library file
true
beta12orEarlier
beta12orEarlier
File of one or more pairs of primer sequences, as used by EMBOSS primersearch application.
primersearch primer pairs sequence record
true
beta12orEarlier
A cluster of protein sequences.
Protein sequence cluster
The sequences are typically related, for example a family of sequences.
Sequence cluster (protein)
beta12orEarlier
A cluster of nucleotide sequences.
Nucleotide sequence cluster
The sequences are typically related, for example a family of sequences.
Sequence cluster (nucleic acid)
beta12orEarlier
The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.
Sequence length
beta12orEarlier
1.5
Size of a sequence word.
Word size is used for example in word-based sequence database search methods.
Word size
true
beta12orEarlier
1.5
Size of a sequence window.
A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.
Window size
true
beta12orEarlier
1.5
Specification of range(s) of length of sequences.
Sequence length range
true
beta12orEarlier
beta12orEarlier
Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.
Sequence information report
true
beta12orEarlier
An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.
Sequence properties report
Sequence property
beta12orEarlier
Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.
Feature record
Features
General sequence features
Sequence features report
SO:0000110
This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required.
Sequence features
http://purl.bioontology.org/ontology/MSH/D058977
beta12orEarlier
beta13
Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Sequence features (comparative)
true
beta12orEarlier
beta12orEarlier
A report of general sequence properties derived from protein sequence data.
Sequence property (protein)
true
beta12orEarlier
beta12orEarlier
A report of general sequence properties derived from nucleotide sequence data.
Sequence property (nucleic acid)
true
beta12orEarlier
A report on sequence complexity, for example low-complexity or repeat regions in sequences.
Sequence property (complexity)
Sequence complexity report
beta12orEarlier
A report on ambiguity in molecular sequence(s).
Sequence property (ambiguity)
Sequence ambiguity report
beta12orEarlier
A report (typically a table) on character or word composition / frequency of a molecular sequence(s).
Sequence composition
Sequence property (composition)
Sequence composition report
beta12orEarlier
A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.
Peptide molecular weight hits
beta12orEarlier
A plot of third base position variability in a nucleotide sequence.
Base position variability plot
beta12orEarlier
beta12orEarlier
A table of character or word composition / frequency of a molecular sequence.
Sequence composition table
true
beta12orEarlier
A table of base frequencies of a nucleotide sequence.
Base frequencies table
beta12orEarlier
A table of word composition of a nucleotide sequence.
Base word frequencies table
beta12orEarlier
A table of amino acid frequencies of a protein sequence.
Sequence composition (amino acid frequencies)
Amino acid frequencies table
beta12orEarlier
A table of amino acid word composition of a protein sequence.
Sequence composition (amino acid words)
Amino acid word frequencies table
beta12orEarlier
beta12orEarlier
Annotation of a molecular sequence in DAS format.
DAS sequence feature annotation
true
beta12orEarlier
Annotation of positional sequence features, organised into a standard feature table.
Sequence feature table
Feature table
beta12orEarlier
A map of (typically one) DNA sequence annotated with positional or non-positional features.
DNA map
Map
beta12orEarlier
An informative report on intrinsic positional features of a nucleotide sequence, formatted to be machine-readable.
Feature table (nucleic acid)
Nucleic acid feature table
Genome features
Genomic features
This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.
Nucleic acid features
beta12orEarlier
An informative report on intrinsic positional features of a protein sequence.
Feature table (protein)
Protein feature table
This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.
Protein features
beta12orEarlier
Moby:GeneticMap
A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.
Linkage map
A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.
Genetic map
beta12orEarlier
A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.
A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.
Sequence map
beta12orEarlier
A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them.
Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.
Physical map
beta12orEarlier
beta12orEarlier
Image of a sequence with matches to signatures, motifs or profiles.
Sequence signature map
true
beta12orEarlier
A map showing banding patterns derived from direct observation of a stained chromosome.
Chromosome map
Cytogenic map
Cytologic map
This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.
Cytogenetic map
beta12orEarlier
A gene map showing distances between loci based on relative cotransduction frequencies.
DNA transduction map
beta12orEarlier
Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene.
Gene map
beta12orEarlier
Sequence map of a plasmid (circular DNA).
Plasmid map
beta12orEarlier
Sequence map of a whole genome.
Genome map
beta12orEarlier
Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.
Restriction map
beta12orEarlier
beta12orEarlier
Image showing matches between protein sequence(s) and InterPro Entries.
The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
InterPro compact match image
true
beta12orEarlier
beta12orEarlier
Image showing detailed information on matches between protein sequence(s) and InterPro Entries.
The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.
InterPro detailed match image
true
beta12orEarlier
beta12orEarlier
Image showing the architecture of InterPro domains in a protein sequence.
The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.
InterPro architecture image
true
beta12orEarlier
beta12orEarlier
SMART protein schematic in PNG format.
SMART protein schematic
true
beta12orEarlier
beta12orEarlier
Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.
GlobPlot domain image
true
beta12orEarlier
1.8
Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.
Sequence motif matches
true
beta12orEarlier
1.5
Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
The report might include derived data map such as classification, annotation, organisation, periodicity etc.
Sequence features (repeats)
true
beta12orEarlier
1.5
A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.
Gene and transcript structure (report)
true
beta12orEarlier
1.8
regions of a nucleic acid sequence containing mobile genetic elements.
Mobile genetic elements
true
beta12orEarlier
1.5
A report on quadruplex-forming motifs in a nucleotide sequence.
Nucleic acid features (quadruplexes)
true
beta12orEarlier
1.8
Report on nucleosome formation potential or exclusion sequence(s).
Nucleosome exclusion sequences
true
beta12orEarlier
beta13
A report on exonic splicing enhancers (ESE) in an exon.
Gene features (exonic splicing enhancer)
true
beta12orEarlier
1.5
A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.
Nucleic acid features (microRNA)
true
beta12orEarlier
1.8
protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.
Coding region
true
beta12orEarlier
beta13
A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.
Gene features (SECIS element)
true
beta12orEarlier
1.8
transcription factor binding sites (TFBS) in a DNA sequence.
Transcription factor binding sites
true
beta12orEarlier
beta12orEarlier
A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.
Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.
Protein features (sites)
true
beta12orEarlier
1.8
signal peptides or signal peptide cleavage sites in protein sequences.
Protein features report (signal peptides)
true
beta12orEarlier
1.8
cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.
Protein features report (cleavage sites)
true
beta12orEarlier
1.8
post-translation modifications in a protein sequence, typically describing the specific sites involved.
Protein features (post-translation modifications)
true
beta12orEarlier
1.8
catalytic residues (active site) of an enzyme.
Protein features report (active sites)
true
beta12orEarlier
1.8
ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.
Protein features report (binding sites)
true
beta12orEarlier
beta13
A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.
Epitope mapping is commonly done during vaccine design.
Protein features (epitopes)
true
beta12orEarlier
1.8
RNA and DNA-binding proteins and binding sites in protein sequences.
Protein features report (nucleic acid binding sites)
true
beta12orEarlier
beta12orEarlier
A report on epitopes that bind to MHC class I molecules.
MHC Class I epitopes report
true
beta12orEarlier
beta12orEarlier
A report on predicted epitopes that bind to MHC class II molecules.
MHC Class II epitopes report
true
beta12orEarlier
beta13
A report or plot of PEST sites in a protein sequence.
'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.
Protein features (PEST sites)
true
beta12orEarlier
beta12orEarlier
Scores from a sequence database search (for example a BLAST search).
Sequence database hits scores list
true
beta12orEarlier
beta12orEarlier
Alignments from a sequence database search (for example a BLAST search).
Sequence database hits alignments list
true
beta12orEarlier
beta12orEarlier
A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).
Sequence database hits evaluation data
true
beta12orEarlier
beta12orEarlier
Alphabet for the motifs (patterns) that MEME will search for.
MEME motif alphabet
true
beta12orEarlier
beta12orEarlier
MEME background frequencies file.
MEME background frequencies file
true
beta12orEarlier
beta12orEarlier
File of directives for ordering and spacing of MEME motifs.
MEME motifs directive file
true
beta12orEarlier
Dirichlet distribution used by hidden Markov model analysis programs.
Dirichlet distribution
beta12orEarlier
1.4
Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states.
HMM emission and transition counts
true
beta12orEarlier
Regular expression pattern.
Regular expression
beta12orEarlier
Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.
Sequence motif
beta12orEarlier
Some type of statistical model representing a (typically multiple) sequence alignment.
Sequence profile
http://semanticscience.org/resource/SIO_010531
beta12orEarlier
An informative report about a specific or conserved protein sequence pattern.
InterPro entry
Protein domain signature
Protein family signature
Protein region signature
Protein repeat signature
Protein site signature
Protein signature
beta12orEarlier
beta12orEarlier
A nucleotide regular expression pattern from the Prosite database.
Prosite nucleotide pattern
true
beta12orEarlier
beta12orEarlier
A protein regular expression pattern from the Prosite database.
Prosite protein pattern
true
beta12orEarlier
A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.
PFM
Position frequency matrix
beta12orEarlier
A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.
PWM
Contributions of individual sequences to the matrix might be uneven (weighted).
Position weight matrix
beta12orEarlier
A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position.
ICM
Information content matrix
beta12orEarlier
A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences.
HMM
Hidden Markov model
beta12orEarlier
One or more fingerprints (sequence classifiers) as used in the PRINTS database.
Fingerprint
beta12orEarlier
beta12orEarlier
A protein signature of the type used in the EMBASSY Signature package.
Domainatrix signature
true
beta12orEarlier
beta12orEarlier
NULL hidden Markov model representation used by the HMMER package.
HMMER NULL hidden Markov model
true
beta12orEarlier
1.5
A protein family signature (sequence classifier) from the InterPro database.
Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures.
Protein family signature
true
beta12orEarlier
1.5
A protein domain signature (sequence classifier) from the InterPro database.
Protein domain signatures identify structural or functional domains or other units with defined boundaries.
Protein domain signature
true
beta12orEarlier
1.5
A protein region signature (sequence classifier) from the InterPro database.
A protein region signature defines a region which cannot be described as a protein family or domain signature.
Protein region signature
true
beta12orEarlier
1.5
A protein repeat signature (sequence classifier) from the InterPro database.
A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.
Protein repeat signature
true
beta12orEarlier
1.5
A protein site signature (sequence classifier) from the InterPro database.
A protein site signature is a classifier for a specific site in a protein.
Protein site signature
true
beta12orEarlier
1.4
A protein conserved site signature (sequence classifier) from the InterPro database.
A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.
Protein conserved site signature
true
beta12orEarlier
1.4
A protein active site signature (sequence classifier) from the InterPro database.
A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.
Protein active site signature
true
beta12orEarlier
1.4
A protein binding site signature (sequence classifier) from the InterPro database.
A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.
Protein binding site signature
true
beta12orEarlier
1.4
A protein post-translational modification signature (sequence classifier) from the InterPro database.
A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.
Protein post-translational modification signature
true
beta12orEarlier
true
Alignment of exactly two molecular sequences.
Sequence alignment (pair)
Pair sequence alignment
http://semanticscience.org/resource/SIO_010068
beta12orEarlier
beta12orEarlier
Alignment of more than two molecular sequences.
Sequence alignment (multiple)
true
beta12orEarlier
Alignment of multiple nucleotide sequences.
Sequence alignment (nucleic acid)
DNA sequence alignment
RNA sequence alignment
Nucleic acid sequence alignment
beta12orEarlier
Alignment of multiple protein sequences.
Sequence alignment (protein)
Protein sequence alignment
beta12orEarlier
Alignment of multiple molecular sequences of different types.
Sequence alignment (hybrid)
Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.
Hybrid sequence alignment
beta12orEarlier
1.12
Alignment of exactly two nucleotide sequences.
Sequence alignment (nucleic acid pair)
true
beta12orEarlier
1.12
Alignment of exactly two protein sequences.
Sequence alignment (protein pair)
true
beta12orEarlier
beta12orEarlier
Alignment of exactly two molecular sequences of different types.
Hybrid sequence alignment (pair)
true
beta12orEarlier
beta12orEarlier
Alignment of more than two nucleotide sequences.
Multiple nucleotide sequence alignment
true
beta12orEarlier
beta12orEarlier
Alignment of more than two protein sequences.
Multiple protein sequence alignment
true
beta12orEarlier
A simple floating point number defining the penalty for opening or extending a gap in an alignment.
Alignment score or penalty
beta12orEarlier
beta12orEarlier
Whether end gaps are scored or not.
Score end gaps control
true
beta12orEarlier
beta12orEarlier
Controls the order of sequences in an output sequence alignment.
Aligned sequence order
true
beta12orEarlier
A penalty for opening a gap in an alignment.
Gap opening penalty
beta12orEarlier
A penalty for extending a gap in an alignment.
Gap extension penalty
beta12orEarlier
A penalty for gaps that are close together in an alignment.
Gap separation penalty
beta12orEarlier
beta12orEarlier
A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
Terminal gap penalty
true
beta12orEarlier
The score for a 'match' used in various sequence database search applications with simple scoring schemes.
Match reward score
beta12orEarlier
The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes.
Mismatch penalty score
beta12orEarlier
This is the threshold drop in score at which extension of word alignment is halted.
Drop off score
beta12orEarlier
beta12orEarlier
A simple floating point number defining the penalty for opening a gap in an alignment.
Gap opening penalty (integer)
true
beta12orEarlier
beta12orEarlier
A simple floating point number defining the penalty for opening a gap in an alignment.
Gap opening penalty (float)
true
beta12orEarlier
beta12orEarlier
A simple floating point number defining the penalty for extending a gap in an alignment.
Gap extension penalty (integer)
true
beta12orEarlier
beta12orEarlier
A simple floating point number defining the penalty for extending a gap in an alignment.
Gap extension penalty (float)
true
beta12orEarlier
beta12orEarlier
A simple floating point number defining the penalty for gaps that are close together in an alignment.
Gap separation penalty (integer)
true
beta12orEarlier
beta12orEarlier
A simple floating point number defining the penalty for gaps that are close together in an alignment.
Gap separation penalty (float)
true
beta12orEarlier
A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
Terminal gap opening penalty
beta12orEarlier
A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
Terminal gap extension penalty
beta12orEarlier
Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.
Sequence identity
beta12orEarlier
Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension.
Data Type is float probably.
Sequence similarity
beta12orEarlier
beta12orEarlier
Data on molecular sequence alignment quality (estimated accuracy).
Sequence alignment metadata (quality report)
true
beta12orEarlier
1.4
Data on character conservation in a molecular sequence alignment.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
Sequence alignment report (site conservation)
true
beta12orEarlier
1.4
Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures.
Sequence alignment report (site correlation)
true
beta12orEarlier
beta12orEarlier
Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).
Sequence-profile alignment (Domainatrix signature)
true
beta12orEarlier
1.5
Alignment of molecular sequence(s) to a hidden Markov model(s).
Sequence-profile alignment (HMM)
true
beta12orEarlier
1.5
Alignment of molecular sequences to a protein fingerprint from the PRINTS database.
Sequence-profile alignment (fingerprint)
true
beta12orEarlier
Continuous quantitative data that may be read during phylogenetic tree calculation.
Phylogenetic continuous quantitative characters
Quantitative traits
Phylogenetic continuous quantitative data
beta12orEarlier
Character data with discrete states that may be read during phylogenetic tree calculation.
Discrete characters
Discretely coded characters
Phylogenetic discrete states
Phylogenetic discrete data
beta12orEarlier
One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny.
Phylogenetic report (cliques)
Phylogenetic character cliques
beta12orEarlier
Phylogenetic invariants data for testing alternative tree topologies.
Phylogenetic report (invariants)
Phylogenetic invariants
beta12orEarlier
1.5
A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.
This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.
Phylogenetic report
true
beta12orEarlier
A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.
Phylogenetic tree report (DNA substitution model)
Sequence alignment report (DNA substitution model)
Substitution model
DNA substitution model
beta12orEarlier
1.4
Data about the shape of a phylogenetic tree.
Phylogenetic tree report (tree shape)
true
beta12orEarlier
1.4
Data on the confidence of a phylogenetic tree.
Phylogenetic tree report (tree evaluation)
true
beta12orEarlier
Distances, such as Branch Score distance, between two or more phylogenetic trees.
Phylogenetic tree report (tree distances)
Phylogenetic tree distances
beta12orEarlier
1.4
Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.
Phylogenetic tree report (tree stratigraphic)
true
beta12orEarlier
Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.
Phylogenetic report (character contrasts)
Phylogenetic character contrasts
beta12orEarlier
beta12orEarlier
Matrix of integer numbers for sequence comparison.
Comparison matrix (integers)
true
beta12orEarlier
beta12orEarlier
Matrix of floating point numbers for sequence comparison.
Comparison matrix (floats)
true
beta12orEarlier
Matrix of integer or floating point numbers for nucleotide comparison.
Nucleotide comparison matrix
Nucleotide substitution matrix
Comparison matrix (nucleotide)
beta12orEarlier
Matrix of integer or floating point numbers for amino acid comparison.
Amino acid comparison matrix
Amino acid substitution matrix
Comparison matrix (amino acid)
beta12orEarlier
beta12orEarlier
Matrix of integer numbers for nucleotide comparison.
Nucleotide substitution matrix (integers)
Nucleotide comparison matrix (integers)
true
beta12orEarlier
beta12orEarlier
Matrix of floating point numbers for nucleotide comparison.
Nucleotide substitution matrix (floats)
Nucleotide comparison matrix (floats)
true
beta12orEarlier
beta12orEarlier
Matrix of integer numbers for amino acid comparison.
Amino acid comparison matrix (integers)
true
beta12orEarlier
beta12orEarlier
Matrix of floating point numbers for amino acid comparison.
Amino acid comparison matrix (floats)
true
beta12orEarlier
3D coordinate and associated data for a nucleic acid tertiary (3D) structure.
Nucleic acid structure
beta12orEarlier
3D coordinate and associated data for a protein tertiary (3D) structure, or part of a structure, possibly in complex with other molecules.
Protein structures
Protein structure
beta12orEarlier
The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.
This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead.
Protein-ligand complex
beta12orEarlier
3D coordinate and associated data for a carbohydrate (3D) structure.
Carbohydrate structure
beta12orEarlier
3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.
CHEBI:23367
Small molecule structure
beta12orEarlier
3D coordinate and associated data for a DNA tertiary (3D) structure.
DNA structure
beta12orEarlier
3D coordinate and associated data for an RNA tertiary (3D) structure.
RNA structure
beta12orEarlier
3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.
tRNA structure
beta12orEarlier
3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.
Protein chain
beta12orEarlier
3D coordinate and associated data for the tertiary (3D) structure of a protein domain.
Protein domain
beta12orEarlier
1.5
3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).
Protein structure (all atoms)
true
beta12orEarlier
3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).
Protein structure (C-alpha atoms)
C-beta atoms from amino acid side-chains may be included.
C-alpha trace
beta12orEarlier
beta12orEarlier
3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).
Protein chain (all atoms)
true
beta12orEarlier
beta12orEarlier
3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).
C-beta atoms from amino acid side-chains may be included.
Protein chain (C-alpha atoms)
true
beta12orEarlier
beta12orEarlier
3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).
Protein domain (all atoms)
true
beta12orEarlier
beta12orEarlier
3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).
C-beta atoms from amino acid side-chains may be included.
Protein domain (C-alpha atoms)
true
beta12orEarlier
Alignment (superimposition) of exactly two molecular tertiary (3D) structures.
Pair structure alignment
Structure alignment (pair)
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of more than two molecular tertiary (3D) structures.
Structure alignment (multiple)
true
beta12orEarlier
Alignment (superimposition) of protein tertiary (3D) structures.
Structure alignment (protein)
Protein structure alignment
beta12orEarlier
Alignment (superimposition) of nucleic acid tertiary (3D) structures.
Structure alignment (nucleic acid)
Nucleic acid structure alignment
beta12orEarlier
1.12
Alignment (superimposition) of exactly two protein tertiary (3D) structures.
Structure alignment (protein pair)
true
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of more than two protein tertiary (3D) structures.
Multiple protein tertiary structure alignment
true
beta12orEarlier
1.5
Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).
Structure alignment (protein all atoms)
true
beta12orEarlier
1.5
Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).
C-beta atoms from amino acid side-chains may be considered.
Structure alignment (protein C-alpha atoms)
true
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).
Pairwise protein tertiary structure alignment (all atoms)
true
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).
C-beta atoms from amino acid side-chains may be included.
Pairwise protein tertiary structure alignment (C-alpha atoms)
true
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).
Multiple protein tertiary structure alignment (all atoms)
true
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).
C-beta atoms from amino acid side-chains may be included.
Multiple protein tertiary structure alignment (C-alpha atoms)
true
beta12orEarlier
1.12
Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.
Structure alignment (nucleic acid pair)
true
beta12orEarlier
beta12orEarlier
Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures.
Multiple nucleic acid tertiary structure alignment
true
beta12orEarlier
Alignment (superimposition) of RNA tertiary (3D) structures.
Structure alignment (RNA)
RNA structure alignment
beta12orEarlier
Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.
Structural transformation matrix
beta12orEarlier
beta12orEarlier
DaliLite hit table of protein chain tertiary structure alignment data.
The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.
DaliLite hit table
true
beta12orEarlier
beta12orEarlier
A score reflecting structural similarities of two molecules.
Molecular similarity score
true
beta12orEarlier
Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.
RMSD
Root-mean-square deviation
beta12orEarlier
A measure of the similarity between two ligand fingerprints.
A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.
Tanimoto similarity score
beta12orEarlier
A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.
3D-1D scoring matrix
beta12orEarlier
A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.
Amino acid index
beta12orEarlier
Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.
Chemical classes (amino acids)
Amino acid index (chemical classes)
beta12orEarlier
Statistical protein contact potentials.
Contact potentials (amino acid pair-wise)
Amino acid pair-wise contact potentials
beta12orEarlier
Molecular weights of amino acids.
Molecular weight (amino acids)
Amino acid index (molecular weight)
beta12orEarlier
Hydrophobic, hydrophilic or charge properties of amino acids.
Hydropathy (amino acids)
Amino acid index (hydropathy)
beta12orEarlier
Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.
White-Wimley data (amino acids)
Amino acid index (White-Wimley data)
beta12orEarlier
Van der Waals radii of atoms for different amino acid residues.
van der Waals radii (amino acids)
Amino acid index (van der Waals radii)
beta12orEarlier
1.5
An informative report on a specific enzyme.
Enzyme report
true
beta12orEarlier
1.5
An informative report on a specific restriction enzyme such as enzyme reference data.
This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.
Restriction enzyme report
true
beta12orEarlier
List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.
The report might include associated data such as frequency of peptide fragment molecular weights.
Peptide molecular weights
beta12orEarlier
Report on the hydrophobic moment of a polypeptide sequence.
Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
Peptide hydrophobic moment
beta12orEarlier
The aliphatic index of a protein.
The aliphatic index is the relative protein volume occupied by aliphatic side chains.
Protein aliphatic index
beta12orEarlier
A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.
Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
Protein sequence hydropathy plot
beta12orEarlier
A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence.
Protein charge plot
beta12orEarlier
The solubility or atomic solvation energy of a protein sequence or structure.
Protein solubility data
Protein solubility
beta12orEarlier
Data on the crystallizability of a protein sequence.
Protein crystallizability data
Protein crystallizability
beta12orEarlier
Data on the stability, intrinsic disorder or globularity of a protein sequence.
Protein globularity data
Protein globularity
beta12orEarlier
The titration curve of a protein.
Protein titration curve
beta12orEarlier
The isoelectric point of one proteins.
Protein isoelectric point
beta12orEarlier
The pKa value of a protein.
Protein pKa value
beta12orEarlier
The hydrogen exchange rate of a protein.
Protein hydrogen exchange rate
beta12orEarlier
The extinction coefficient of a protein.
Protein extinction coefficient
beta12orEarlier
The optical density of a protein.
Protein optical density
beta12orEarlier
beta13
An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).
Protein report (subcellular localisation)
Protein subcellular localisation
true
beta12orEarlier
An report on allergenicity / immunogenicity of peptides and proteins.
Peptide immunogenicity
Peptide immunogenicity report
This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
Peptide immunogenicity data
beta12orEarlier
beta13
A report on the immunogenicity of MHC class I or class II binding peptides.
MHC peptide immunogenicity report
true
beta12orEarlier
A human-readable collection of information about one or more specific protein 3D structure(s) or structural domains.
Protein property (structural)
Protein report (structure)
Protein structural property
Protein structure report (domain)
Protein structure-derived report
Protein structure report
beta12orEarlier
Report on the quality of a protein three-dimensional model.
Protein property (structural quality)
Protein report (structural quality)
Protein structure report (quality evaluation)
Protein structure validation report
Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.
Protein structural quality report
beta12orEarlier
1.12
Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups.
Protein non-covalent interactions report
true
beta12orEarlier
1.4
Informative report on flexibility or motion of a protein structure.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein flexibility or motion report
true
beta12orEarlier
Data on the solvent accessible or buried surface area of a protein structure.
This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.
Protein solvent accessibility
beta12orEarlier
1.4
Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein surface report
true
beta12orEarlier
Phi/psi angle data or a Ramachandran plot of a protein structure.
Ramachandran plot
beta12orEarlier
Data on the net charge distribution (dipole moment) of a protein structure.
Protein dipole moment
beta12orEarlier
A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.
Protein distance matrix
beta12orEarlier
An amino acid residue contact map for a protein structure.
Protein contact map
beta12orEarlier
Report on clusters of contacting residues in protein structures such as a key structural residue network.
Protein residue 3D cluster
beta12orEarlier
Patterns of hydrogen bonding in protein structures.
Protein hydrogen bonds
beta12orEarlier
1.4
Non-canonical atomic interactions in protein structures.
Protein non-canonical interactions
true
beta12orEarlier
1.5
Information on a node from the CATH database.
The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.
CATH node
true
beta12orEarlier
1.5
Information on a node from the SCOP database.
SCOP node
true
beta12orEarlier
beta12orEarlier
An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.
EMBASSY domain classification
true
beta12orEarlier
1.5
Information on a protein 'class' node from the CATH database.
CATH class
true
beta12orEarlier
1.5
Information on a protein 'architecture' node from the CATH database.
CATH architecture
true
beta12orEarlier
1.5
Information on a protein 'topology' node from the CATH database.
CATH topology
true
beta12orEarlier
1.5
Information on a protein 'homologous superfamily' node from the CATH database.
CATH homologous superfamily
true
beta12orEarlier
1.5
Information on a protein 'structurally similar group' node from the CATH database.
CATH structurally similar group
true
beta12orEarlier
1.5
Information on a protein 'functional category' node from the CATH database.
CATH functional category
true
beta12orEarlier
beta12orEarlier
A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s).
Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
Protein fold recognition report
true
beta12orEarlier
1.8
protein-protein interaction(s), including interactions between protein domains.
Protein-protein interaction report
true
beta12orEarlier
An informative report on protein-ligand (small molecule) interaction(s).
Protein-drug interaction report
Protein-ligand interaction report
beta12orEarlier
1.8
protein-DNA/RNA interaction(s).
Protein-nucleic acid interactions report
true
beta12orEarlier
Nucleic acid melting curve: a melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the proportion of nucleic acid which are double-stranded versus temperature.
Nucleic acid probability profile: a probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature
Nucleic acid stitch profile: stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.
Nucleic acid temperature profile: a temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Plots melting temperature versus base position.
Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.
Nucleic acid stability profile
Melting map
Nucleic acid melting curve
A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.
Nucleic acid melting profile
beta12orEarlier
Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
Nucleic acid enthalpy
beta12orEarlier
Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
Nucleic acid entropy
beta12orEarlier
beta12orEarlier
Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
Nucleic acid melting temperature
true
beta12orEarlier
1.21
Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA).
Nucleic acid stitch profile
true
beta12orEarlier
DNA base pair stacking energies data.
DNA base pair stacking energies data
beta12orEarlier
DNA base pair twist angle data.
DNA base pair twist angle data
beta12orEarlier
DNA base trimer roll angles data.
DNA base trimer roll angles data
beta12orEarlier
beta12orEarlier
RNA parameters used by the Vienna package.
Vienna RNA parameters
true
beta12orEarlier
beta12orEarlier
Structure constraints used by the Vienna package.
Vienna RNA structure constraints
true
beta12orEarlier
beta12orEarlier
RNA concentration data used by the Vienna package.
Vienna RNA concentration data
true
beta12orEarlier
beta12orEarlier
RNA calculated energy data generated by the Vienna package.
Vienna RNA calculated energy
true
beta12orEarlier
Dotplot of RNA base pairing probability matrix.
Such as generated by the Vienna package.
Base pairing probability matrix dotplot
beta12orEarlier
A human-readable collection of information about RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.
Nucleic acid report (folding model)
Nucleic acid report (folding)
RNA secondary structure folding classification
RNA secondary structure folding probablities
Nucleic acid folding report
beta12orEarlier
Table of codon usage data calculated from one or more nucleic acid sequences.
A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.
Codon usage table
beta12orEarlier
A genetic code for an organism.
A genetic code need not include detailed codon usage information.
Genetic code
beta12orEarlier
beta12orEarlier
A simple measure of synonymous codon usage bias often used to predict gene expression levels.
Codon adaptation index
true
beta12orEarlier
A plot of the synonymous codon usage calculated for windows over a nucleotide sequence.
Synonymous codon usage statistic plot
Codon usage bias plot
beta12orEarlier
beta12orEarlier
The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons.
Nc statistic
true
beta12orEarlier
The differences in codon usage fractions between two codon usage tables.
Codon usage fraction difference
beta12orEarlier
A human-readable collection of information about the influence of genotype on drug response.
The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
Pharmacogenomic test report
beta12orEarlier
A human-readable collection of information about a specific disease.
For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.
Disease report
beta12orEarlier
1.8
A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
Linkage disequilibrium (report)
true
beta12orEarlier
A graphical 2D tabular representation of expression data, typically derived from an omics experiment. A heat map is a table where rows and columns correspond to different features and contexts (for example, cells or samples) and the cell colour represents the level of expression of a gene that context.
Heat map
beta12orEarlier
beta12orEarlier
Affymetrix library file of information about which probes belong to which probe set.
Affymetrix probe sets library file
true
beta12orEarlier
beta12orEarlier
Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.
GIN file
Affymetrix probe sets information library file
true
beta12orEarlier
1.12
Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.
Molecular weights standard fingerprint
true
beta12orEarlier
1.8
A report typically including a map (diagram) of a metabolic pathway.
This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
Metabolic pathway report
true
beta12orEarlier
1.8
genetic information processing pathways.
Genetic information processing pathway report
true
beta12orEarlier
1.8
environmental information processing pathways.
Environmental information processing pathway report
true
beta12orEarlier
1.8
A report typically including a map (diagram) of a signal transduction pathway.
Signal transduction pathway report
true
beta12orEarlier
1.8
Topic concernning cellular process pathways.
Cellular process pathways report
true
beta12orEarlier
1.8
disease pathways, typically of human disease.
Disease pathway or network report
true
beta12orEarlier
1.21
A report typically including a map (diagram) of drug structure relationships.
Drug structure relationship map
true
beta12orEarlier
1.8
networks of protein interactions.
Protein interaction networks
true
beta12orEarlier
1.5
An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.
A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.
MIRIAM datatype
true
beta12orEarlier
A simple floating point number defining the lower or upper limit of an expectation value (E-value).
Expectation value
An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.
E-value
beta12orEarlier
The z-value is the number of standard deviations a data value is above or below a mean value.
A z-value might be specified as a threshold for reporting hits from database searches.
Z-value
beta12orEarlier
The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true.
A z-value might be specified as a threshold for reporting hits from database searches.
P-value
beta12orEarlier
1.5
Information on a database (or ontology) version, for example name, version number and release date.
Database version information
true
beta12orEarlier
1.5
Information on an application version, for example name, version number and release date.
Tool version information
true
beta12orEarlier
beta12orEarlier
Information on a version of the CATH database.
CATH version information
true
beta12orEarlier
beta12orEarlier
Cross-mapping of Swiss-Prot codes to PDB identifiers.
Swiss-Prot to PDB mapping
true
beta12orEarlier
beta12orEarlier
Cross-references from a sequence record to other databases.
Sequence database cross-references
true
beta12orEarlier
1.5
Metadata on the status of a submitted job.
Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).
Job status
true
beta12orEarlier
1.0
The (typically numeric) unique identifier of a submitted job.
Job ID
true
beta12orEarlier
1.5
A label (text token) describing the type of job, for example interactive or non-interactive.
Job type
true
beta12orEarlier
1.5
A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.
Tool log
true
beta12orEarlier
beta12orEarlier
DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.
DaliLite log file
true
beta12orEarlier
beta12orEarlier
STRIDE log file.
STRIDE log file
true
beta12orEarlier
beta12orEarlier
NACCESS log file.
NACCESS log file
true
beta12orEarlier
beta12orEarlier
EMBOSS wordfinder log file.
EMBOSS wordfinder log file
true
beta12orEarlier
beta12orEarlier
EMBOSS (EMBASSY) domainatrix application log file.
EMBOSS domainatrix log file
true
beta12orEarlier
beta12orEarlier
EMBOSS (EMBASSY) sites application log file.
EMBOSS sites log file
true
beta12orEarlier
beta12orEarlier
EMBOSS (EMBASSY) supermatcher error file.
EMBOSS supermatcher error file
true
beta12orEarlier
beta12orEarlier
EMBOSS megamerger log file.
EMBOSS megamerger log file
true
beta12orEarlier
beta12orEarlier
EMBOSS megamerger log file.
EMBOSS whichdb log file
true
beta12orEarlier
beta12orEarlier
EMBOSS vectorstrip log file.
EMBOSS vectorstrip log file
true
beta12orEarlier
A username on a computer system.
Username
beta12orEarlier
A password on a computer system.
Password
beta12orEarlier
Moby:Email
Moby:EmailAddress
A valid email address of an end-user.
Email address
beta12orEarlier
The name of a person.
Person name
beta12orEarlier
1.5
Number of iterations of an algorithm.
Number of iterations
true
beta12orEarlier
1.5
Number of entities (for example database hits, sequences, alignments etc) to write to an output file.
Number of output entities
true
beta12orEarlier
beta12orEarlier
Controls the order of hits (reported matches) in an output file from a database search.
Hit sort order
true
beta12orEarlier
A drug structure relationship map is report (typically a map diagram) of drug structure relationships.
A human-readable collection of information about a specific drug.
Drug annotation
Drug structure relationship map
Drug report
beta12orEarlier
An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information.
See also 'Phylogenetic tree'
Phylogenetic tree image
beta12orEarlier
Image of RNA secondary structure, knots, pseudoknots etc.
RNA secondary structure image
beta12orEarlier
Image of protein secondary structure.
Protein secondary structure image
beta12orEarlier
Image of one or more molecular tertiary (3D) structures.
Structure image
beta12orEarlier
Image of two or more aligned molecular sequences possibly annotated with alignment features.
Sequence alignment image
beta12orEarlier
An image of the structure of a small chemical compound.
Small molecule structure image
Chemical structure sketch
Small molecule sketch
The molecular identifier and formula are typically included.
Chemical structure image
beta12orEarlier
A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.
Fate map
beta12orEarlier
An image of spots from a microarray experiment.
Microarray spots image
beta12orEarlier
beta12orEarlier
A term from the BioPax ontology.
BioPax term
true
beta12orEarlier
beta12orEarlier
A term definition from The Gene Ontology (GO).
GO
true
beta12orEarlier
beta12orEarlier
A term from the MeSH vocabulary.
MeSH
true
beta12orEarlier
beta12orEarlier
A term from the HGNC controlled vocabulary.
HGNC
true
beta12orEarlier
beta12orEarlier
A term from the NCBI taxonomy vocabulary.
NCBI taxonomy vocabulary
true
beta12orEarlier
beta12orEarlier
A term from the Plant Ontology (PO).
Plant ontology term
true
beta12orEarlier
beta12orEarlier
A term from the UMLS vocabulary.
UMLS
true
beta12orEarlier
beta12orEarlier
A term from Foundational Model of Anatomy.
Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
FMA
true
beta12orEarlier
beta12orEarlier
A term from the EMAP mouse ontology.
EMAP
true
beta12orEarlier
beta12orEarlier
A term from the ChEBI ontology.
ChEBI
true
beta12orEarlier
beta12orEarlier
A term from the MGED ontology.
MGED
true
beta12orEarlier
beta12orEarlier
A term from the myGrid ontology.
The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
myGrid
true
beta12orEarlier
beta12orEarlier
A term definition for a biological process from the Gene Ontology (GO).
Data Type is an enumerated string.
GO (biological process)
true
beta12orEarlier
beta12orEarlier
A term definition for a molecular function from the Gene Ontology (GO).
Data Type is an enumerated string.
GO (molecular function)
true
beta12orEarlier
beta12orEarlier
A term definition for a cellular component from the Gene Ontology (GO).
Data Type is an enumerated string.
GO (cellular component)
true
beta12orEarlier
1.5
A relation type defined in an ontology.
Ontology relation type
true
beta12orEarlier
The definition of a concept from an ontology.
Ontology class definition
Ontology concept definition
beta12orEarlier
1.4
A comment on a concept from an ontology.
Ontology concept comment
true
beta12orEarlier
beta12orEarlier
Reference for a concept from an ontology.
Ontology concept reference
true
beta12orEarlier
beta12orEarlier
Information on a published article provided by the doc2loc program.
The doc2loc output includes the url, format, type and availability code of a document for every service provider.
doc2loc document information
true
beta12orEarlier
PDBML:PDB_residue_no
WHATIF: pdb_number
A residue identifier (a string) from a PDB file.
PDB residue number
beta12orEarlier
Cartesian coordinate of an atom (in a molecular structure).
Cartesian coordinate
Atomic coordinate
beta12orEarlier
1.21
PDBML:_atom_site.Cartn_x in PDBML
WHATIF: PDBx_Cartn_x
Cartesian x coordinate of an atom (in a molecular structure).
Cartesian x coordinate
Atomic x coordinate
true
beta12orEarlier
1.21
PDBML:_atom_site.Cartn_y in PDBML
WHATIF: PDBx_Cartn_y
Cartesian y coordinate of an atom (in a molecular structure).
Cartesian y coordinate
Atomic y coordinate
true
beta12orEarlier
1.21
PDBML:_atom_site.Cartn_z
WHATIF: PDBx_Cartn_z
Cartesian z coordinate of an atom (in a molecular structure).
Cartesian z coordinate
Atomic z coordinate
true
beta12orEarlier
PDBML:pdbx_PDB_atom_name
WHATIF: PDBx_auth_atom_id
WHATIF: PDBx_type_symbol
WHATIF: alternate_atom
WHATIF: atom_type
Identifier (a string) of a specific atom from a PDB file for a molecular structure.
PDB atom name
beta12orEarlier
Data on a single atom from a protein structure.
Atom data
CHEBI:33250
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein atom
beta12orEarlier
Data on a single amino acid residue position in a protein structure.
Residue
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein residue
beta12orEarlier
Name of an atom.
Atom name
beta12orEarlier
WHATIF: type
Three-letter amino acid residue names as used in PDB files.
PDB residue name
beta12orEarlier
PDBML:pdbx_PDB_model_num
WHATIF: model_number
Identifier of a model structure from a PDB file.
Model number
PDB model number
beta12orEarlier
beta13
Summary of domain classification information for a CATH domain.
The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
CATH domain report
true
beta12orEarlier
beta12orEarlier
FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).
CATH representative domain sequences (ATOM)
true
beta12orEarlier
beta12orEarlier
FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).
CATH representative domain sequences (COMBS)
true
beta12orEarlier
beta12orEarlier
FASTA sequence database for all CATH domains (based on PDB ATOM records).
CATH domain sequences (ATOM)
true
beta12orEarlier
beta12orEarlier
FASTA sequence database for all CATH domains (based on COMBS sequence data).
CATH domain sequences (COMBS)
true
beta12orEarlier
Information on an molecular sequence version.
Sequence version information
Sequence version
beta12orEarlier
A numerical value, that is some type of scored value arising for example from a prediction method.
Score
beta12orEarlier
beta13
Report on general functional properties of specific protein(s).
For properties that can be mapped to a sequence, use 'Sequence report' instead.
Protein report (function)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS
Name of a gene from Aspergillus Genome Database.
Gene name (ASPGD)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS
Name of a gene from Candida Genome Database.
Gene name (CGD)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase
Name of a gene from dictyBase database.
Gene name (dictyBase)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G
Primary name of a gene from EcoGene Database.
EcoGene primary gene name
Gene name (EcoGene primary)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus
Name of a gene from MaizeGDB (maize genes) database.
Gene name (MaizeGDB)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS
Name of a gene from Saccharomyces Genome Database.
Gene name (SGD)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS
Name of a gene from Tetrahymena Genome Database.
Gene name (TGD)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs: CGSC
Symbol of a gene from E.coli Genetic Stock Center.
Gene name (CGSC)
true
beta12orEarlier
1.3
HGNC:[0-9]{1,5}
http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene
Symbol of a gene approved by the HUGO Gene Nomenclature Committee.
Gene name (HGNC)
true
beta12orEarlier
1.3
MGI:[0-9]+
http://www.geneontology.org/doc/GO.xrf_abbs: MGD
Symbol of a gene from the Mouse Genome Database.
Gene name (MGD)
true
beta12orEarlier
1.3
http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG
Symbol of a gene from Bacillus subtilis Genome Sequence Project.
Gene name (Bacillus subtilis)
true
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB
Identifier of a gene from PlasmoDB Plasmodium Genome Resource.
Gene ID (PlasmoDB)
beta12orEarlier
Identifier of a gene from EcoGene Database.
EcoGene Accession
EcoGene ID
Gene ID (EcoGene)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: FB
http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase
Gene identifier from FlyBase database.
Gene ID (FlyBase)
beta12orEarlier
beta13
Gene identifier from Glossina morsitans GeneDB database.
Gene ID (GeneDB Glossina morsitans)
true
beta12orEarlier
beta13
Gene identifier from Leishmania major GeneDB database.
Gene ID (GeneDB Leishmania major)
true
beta12orEarlier
beta13
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum
Gene identifier from Plasmodium falciparum GeneDB database.
Gene ID (GeneDB Plasmodium falciparum)
true
beta12orEarlier
beta13
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe
Gene identifier from Schizosaccharomyces pombe GeneDB database.
Gene ID (GeneDB Schizosaccharomyces pombe)
true
beta12orEarlier
beta13
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei
Gene identifier from Trypanosoma brucei GeneDB database.
Gene ID (GeneDB Trypanosoma brucei)
true
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE
http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene
Gene identifier from Gramene database.
Gene ID (Gramene)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD
http://www.geneontology.org/doc/GO.xrf_abbs: VMD
Gene identifier from Virginia Bioinformatics Institute microbial database.
Gene ID (Virginia microbial)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: SGN
Gene identifier from Sol Genomics Network.
Gene ID (SGN)
beta12orEarlier
WBGene[0-9]{8}
http://www.geneontology.org/doc/GO.xrf_abbs: WB
http://www.geneontology.org/doc/GO.xrf_abbs: WormBase
Gene identifier used by WormBase database.
Gene ID (WormBase)
beta12orEarlier
beta12orEarlier
Any name (other than the recommended one) for a gene.
Gene synonym
true
beta12orEarlier
The name of an open reading frame attributed by a sequencing project.
ORF name
beta12orEarlier
beta12orEarlier
A component of a larger sequence assembly.
Sequence assembly component
true
beta12orEarlier
beta12orEarlier
A report on a chromosome aberration such as abnormalities in chromosome structure.
Chromosome annotation (aberration)
true
beta12orEarlier
true
An identifier of a clone (cloned molecular sequence) from a database.
Clone ID
beta12orEarlier
PDBML:pdbx_PDB_ins_code
WHATIF: insertion_code
An insertion code (part of the residue number) for an amino acid residue from a PDB file.
PDB insertion code
beta12orEarlier
WHATIF: PDBx_occupancy
The fraction of an atom type present at a site in a molecular structure.
The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.
Atomic occupancy
beta12orEarlier
WHATIF: PDBx_B_iso_or_equiv
Isotropic B factor (atomic displacement parameter) for an atom from a PDB file.
Isotropic B factor
beta12orEarlier
A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.
Deletion-based cytogenetic map
A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.
Deletion map
beta12orEarlier
A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.
Quantitative trait locus map
QTL map
beta12orEarlier
Moby:Haplotyping_Study_obj
A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.
Haplotype map
beta12orEarlier
1.21
Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.
Map set data
true
beta12orEarlier
beta12orEarlier
A feature which may mapped (positioned) on a genetic or other type of map.
Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.
Map feature
true
beta12orEarlier
1.5
A designation of the type of map (genetic map, physical map, sequence map etc) or map set.
Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.
Map type
true
beta12orEarlier
The name of a protein fold.
Protein fold name
beta12orEarlier
Moby:BriefTaxonConcept
Moby:PotentialTaxon
The name of a group of organisms belonging to the same taxonomic rank.
Taxonomic rank
Taxonomy rank
For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
Taxon
beta12orEarlier
true
A unique identifier of a (group of) organisms.
Organism identifier
beta12orEarlier
The name of a genus of organism.
Genus name
beta12orEarlier
Moby:GCP_Taxon
Moby:TaxonName
Moby:TaxonScientificName
Moby:TaxonTCS
Moby:iANT_organism-xml
The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.
Taxonomic information
Taxonomic name
Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.
Taxonomic classification
beta12orEarlier
Moby_namespace:iHOPorganism
A unique identifier for an organism used in the iHOP database.
iHOP organism ID
beta12orEarlier
Common name for an organism as used in the GenBank database.
Genbank common name
beta12orEarlier
The name of a taxon from the NCBI taxonomy database.
NCBI taxon
beta12orEarlier
beta12orEarlier
An alternative for a word.
Synonym
true
beta12orEarlier
beta12orEarlier
A common misspelling of a word.
Misspelling
true
beta12orEarlier
beta12orEarlier
An abbreviation of a phrase or word.
Acronym
true
beta12orEarlier
beta12orEarlier
A term which is likely to be misleading of its meaning.
Misnomer
true
beta12orEarlier
Moby:Author
Information on the authors of a published work.
Author ID
beta12orEarlier
An identifier representing an author in the DragonDB database.
DragonDB author identifier
beta12orEarlier
Moby:DescribedLink
A URI along with annotation describing the data found at the address.
Annotated URI
beta12orEarlier
beta12orEarlier
A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.
UniProt keywords
true
beta12orEarlier
Moby_namespace:GENEFARM_GeneID
Identifier of a gene from the GeneFarm database.
Gene ID (GeneFarm)
beta12orEarlier
Moby_namespace:Blattner_number
The blattner identifier for a gene.
Blattner number
beta12orEarlier
beta13
Moby_namespace:MIPS_GE_Maize
Identifier for genetic elements in MIPS Maize database.
Gene ID (MIPS Maize)
true
beta12orEarlier
beta13
Moby_namespace:MIPS_GE_Medicago
Identifier for genetic elements in MIPS Medicago database.
Gene ID (MIPS Medicago)
true
beta12orEarlier
1.3
Moby_namespace:DragonDB_Gene
The name of an Antirrhinum Gene from the DragonDB database.
Gene name (DragonDB)
true
beta12orEarlier
1.3
A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.
Gene name (Arabidopsis)
true
beta12orEarlier
Moby_namespace:iHOPsymbol
A unique identifier of a protein or gene used in the iHOP database.
iHOP symbol
beta12orEarlier
1.3
Name of a gene from the GeneFarm database.
GeneFarm gene ID
Gene name (GeneFarm)
true
beta12orEarlier
true
A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.
Locus identifier
Locus name
Locus ID
beta12orEarlier
AT[1-5]G[0-9]{5}
http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode
Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)
AGI ID
AGI identifier
AGI locus code
Arabidopsis gene loci number
Locus ID (AGI)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD
http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID
Identifier for loci from ASPGD (Aspergillus Genome Database).
Locus ID (ASPGD)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG
Identifier for loci from Magnaporthe grisea Database at the Broad Institute.
Locus ID (MGG)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: CGD
http://www.geneontology.org/doc/GO.xrf_abbs: CGDID
Identifier for loci from CGD (Candida Genome Database).
CGD locus identifier
CGDID
Locus ID (CGD)
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR
http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR
Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.
Locus ID (CMR)
beta12orEarlier
Moby_namespace:LocusID
http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag
Identifier for loci from NCBI database.
Locus ID (NCBI)
NCBI locus tag
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: SGD
http://www.geneontology.org/doc/GO.xrf_abbs: SGDID
Identifier for loci from SGD (Saccharomyces Genome Database).
SGDID
Locus ID (SGD)
beta12orEarlier
Moby_namespace:MMP_Locus
Identifier of loci from Maize Mapping Project.
Locus ID (MMP)
beta12orEarlier
Moby_namespace:DDB_gene
Identifier of locus from DictyBase (Dictyostelium discoideum).
Locus ID (DictyBase)
beta12orEarlier
Moby_namespace:EntrezGene_EntrezGeneID
Moby_namespace:EntrezGene_ID
Identifier of a locus from EntrezGene database.
Locus ID (EntrezGene)
beta12orEarlier
Moby_namespace:MaizeGDB_Locus
Identifier of locus from MaizeGDB (Maize genome database).
Locus ID (MaizeGDB)
beta12orEarlier
beta12orEarlier
Moby:SO_QTL
A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment).
A QTL sometimes but does not necessarily correspond to a gene.
Quantitative trait locus
true
beta12orEarlier
Moby_namespace:GeneId
Identifier of a gene from the KOME database.
Gene ID (KOME)
beta12orEarlier
Moby:Tropgene_locus
Identifier of a locus from the Tropgene database.
Locus ID (Tropgene)
beta12orEarlier
true
An alignment of molecular sequences, structures or profiles derived from them.
Alignment
beta12orEarlier
Data for an atom (in a molecular structure).
General atomic property
Atomic property
beta12orEarlier
Moby_namespace:SP_KW
http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW
A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.
UniProt keyword
beta12orEarlier
beta12orEarlier
A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.
Ordered locus name
true
beta12orEarlier
Moby:GCP_MapInterval
Moby:GCP_MapPoint
Moby:GCP_MapPosition
Moby:GenePosition
Moby:HitPosition
Moby:Locus
Moby:MapPosition
Moby:Position
PDBML:_atom_site.id
A position in a map (for example a genetic map), either a single position (point) or a region / interval.
Locus
Map position
Sequence co-ordinates
This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.
Sequence coordinates
beta12orEarlier
Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.
Amino acid data
Amino acid property
beta12orEarlier
beta13
A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.
This is a broad data type and is used a placeholder for other, more specific types.
Annotation
true
beta12orEarlier
Data describing a molecular map (genetic or physical) or a set of such maps, including various attributes of, data extracted from or derived from the analysis of them, but exluding the map(s) themselves. This includes metadata for map sets that share a common set of features which are mapped.
Map attribute
Map set data
Map data
beta12orEarlier
beta12orEarlier
Data used by the Vienna RNA analysis package.
Vienna RNA structural data
true
beta12orEarlier
1.5
Data used to replace (mask) characters in a molecular sequence.
Sequence mask parameter
true
beta12orEarlier
Data concerning chemical reaction(s) catalysed by enzyme(s).
This is a broad data type and is used a placeholder for other, more specific types.
Enzyme kinetics data
beta12orEarlier
A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent.
Michaelis Menten plot
beta12orEarlier
A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v).
Hanes Woolf plot
beta12orEarlier
beta13
Raw data from or annotation on laboratory experiments.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Experimental data
true
beta12orEarlier
1.5
Information on a genome version.
Genome version information
true
beta12orEarlier
Typically a human-readable summary of body of facts or information indicating why a statement is true or valid. This may include a computational prediction, laboratory experiment, literature reference etc.
Evidence
beta12orEarlier
1.8
A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
Sequence record lite
true
beta12orEarlier
One or more molecular sequences, possibly with associated annotation.
Sequences
This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
Sequence
http://purl.bioontology.org/ontology/MSH/D008969
http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation
beta12orEarlier
1.8
A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
Nucleic acid sequence record (lite)
true
beta12orEarlier
1.8
A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
Sequence record lite (protein)
Protein sequence record (lite)
true
beta12orEarlier
A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.
Document
Record
You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.
Report
http://semanticscience.org/resource/SIO_000148
beta12orEarlier
General data for a molecule.
General molecular property
Molecular property (general)
beta12orEarlier
beta13
Data concerning molecular structural data.
This is a broad data type and is used a placeholder for other, more specific types.
Structural data
true
beta12orEarlier
A nucleotide sequence motif.
Nucleic acid sequence motif
DNA sequence motif
RNA sequence motif
Sequence motif (nucleic acid)
beta12orEarlier
An amino acid sequence motif.
Protein sequence motif
Sequence motif (protein)
beta12orEarlier
1.5
Some simple value controlling a search operation, typically a search of a database.
Search parameter
true
beta12orEarlier
A report of hits from searching a database of some type.
Database hits
Search results
Database search results
beta12orEarlier
1.5
The secondary structure assignment (predicted or real) of a nucleic acid or protein.
Secondary structure
true
beta12orEarlier
An array of numerical values.
Array
This is a broad data type and is used a placeholder for other, more specific types.
Matrix
beta12orEarlier
1.8
Data concerning, extracted from, or derived from the analysis of molecular alignment of some type.
This is a broad data type and is used a placeholder for other, more specific types.
Alignment data
true
beta12orEarlier
A human-readable collection of information about one or more specific nucleic acid molecules.
Nucleic acid report
beta12orEarlier
A human-readable collection of information about one or more molecular tertiary (3D) structures. It might include annotation on the structure, a computer-generated report of analysis of structural data, and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.
Structure-derived report
Structure report
beta12orEarlier
1.21
A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s).
Nucleic acid structure data
true
beta12orEarlier
A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.
Physicochemical property
SO:0000400
Molecular property
beta12orEarlier
Structural data for DNA base pairs or runs of bases, such as energy or angle data.
DNA base structural data
beta12orEarlier
1.5
Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on.
Database entry version information
true
beta12orEarlier
true
A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.
Accession
http://semanticscience.org/resource/SIO_000675
http://semanticscience.org/resource/SIO_000731
beta12orEarlier
1.8
single nucleotide polymorphism (SNP) in a DNA sequence.
SNP
true
beta12orEarlier
Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.
A list of database accessions or identifiers are usually included.
Data reference
beta12orEarlier
true
An identifier of a submitted job.
Job identifier
http://wsio.org/data_009
beta12orEarlier
true
A name of a thing, which need not necessarily uniquely identify it.
Symbolic name
Name
"http://www.w3.org/2000/01/rdf-schema#label
http://semanticscience.org/resource/SIO_000116
http://usefulinc.com/ns/doap#name
Closely related, but focusing on labeling and human readability but not on identification.
beta12orEarlier
1.5
A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).
Type
http://purl.org/dc/elements/1.1/type
true
beta12orEarlier
An identifier of a software end-user (typically a person).
User ID
beta12orEarlier
A three-letter code used in the KEGG databases to uniquely identify organisms.
KEGG organism code
beta12orEarlier
1.3
[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*
Moby_namespace:GeneId
Name of an entry (gene) from the KEGG GENES database.
Gene name (KEGG GENES)
true
beta12orEarlier
Identifier of an object from one of the BioCyc databases.
BioCyc ID
beta12orEarlier
Identifier of a compound from the BioCyc chemical compounds database.
BioCyc compound ID
BioCyc compound identifier
Compound ID (BioCyc)
beta12orEarlier
Identifier of a biological reaction from the BioCyc reactions database.
Reaction ID (BioCyc)
beta12orEarlier
Identifier of an enzyme from the BioCyc enzymes database.
BioCyc enzyme ID
Enzyme ID (BioCyc)
beta12orEarlier
true
Identifier of a biological reaction from a database.
Reaction ID
beta12orEarlier
true
An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).
This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
Identifier (hybrid)
beta12orEarlier
true
Identifier of a molecular property.
Molecular property identifier
beta12orEarlier
true
Identifier of a codon usage table, for example a genetic code.
Codon usage table identifier
Codon usage table ID
beta12orEarlier
Primary identifier of an object from the FlyBase database.
FlyBase primary identifier
beta12orEarlier
Identifier of an object from the WormBase database.
WormBase identifier
beta12orEarlier
CE[0-9]{5}
Protein identifier used by WormBase database.
WormBase wormpep ID
beta12orEarlier
beta12orEarlier
An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon.
Nucleic acid features (codon)
true
beta12orEarlier
true
An identifier of a map of a molecular sequence.
Map identifier
beta12orEarlier
true
An identifier of a software end-user (typically a person).
Person identifier
beta12orEarlier
true
Name or other identifier of a nucleic acid molecule.
Nucleic acid identifier
beta12orEarlier
1.20
Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).
Translation frame specification
true
beta12orEarlier
true
An identifier of a genetic code.
Genetic code identifier
beta12orEarlier
Informal name for a genetic code, typically an organism name.
Genetic code name
beta12orEarlier
Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.
File format name
beta12orEarlier
1.5
A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.
Sequence profile type
true
beta12orEarlier
Name of a computer operating system such as Linux, PC or Mac.
Operating system name
beta12orEarlier
beta12orEarlier
A type of point or block mutation, including insertion, deletion, change, duplication and moves.
Mutation type
true
beta12orEarlier
A logical operator such as OR, AND, XOR, and NOT.
Logical operator
beta12orEarlier
1.5
A control of the order of data that is output, for example the order of sequences in an alignment.
Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.
Results sort order
true
beta12orEarlier
beta12orEarlier
A simple parameter that is a toggle (boolean value), typically a control for a modal tool.
Toggle
true
beta12orEarlier
beta12orEarlier
The width of an output sequence or alignment.
Sequence width
true
beta12orEarlier
A penalty for introducing or extending a gap in an alignment.
Gap penalty
beta12orEarlier
A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.
Melting temperature
Nucleic acid melting temperature
beta12orEarlier
The concentration of a chemical compound.
Concentration
beta12orEarlier
1.5
Size of the incremental 'step' a sequence window is moved over a sequence.
Window step size
true
beta12orEarlier
beta12orEarlier
An image of a graph generated by the EMBOSS suite.
EMBOSS graph
true
beta12orEarlier
beta12orEarlier
An application report generated by the EMBOSS suite.
EMBOSS report
true
beta12orEarlier
1.5
An offset for a single-point sequence position.
Sequence offset
true
beta12orEarlier
1.5
A value that serves as a threshold for a tool (usually to control scoring or output).
Threshold
true
beta12orEarlier
beta13
An informative report on a transcription factor protein.
This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.
Protein report (transcription factor)
true
beta12orEarlier
beta12orEarlier
The name of a category of biological or bioinformatics database.
Database category name
true
beta12orEarlier
beta12orEarlier
Name of a sequence profile.
Sequence profile name
true
beta12orEarlier
beta12orEarlier
Specification of one or more colors.
Color
true
beta12orEarlier
1.5
A parameter that is used to control rendering (drawing) to a device or image.
Rendering parameter
true
beta12orEarlier
Any arbitrary name of a molecular sequence.
Sequence name
beta12orEarlier
1.5
A temporal date.
Date
true
beta12orEarlier
beta12orEarlier
Word composition data for a molecular sequence.
Word composition
true
beta12orEarlier
A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.
Fickett testcode plot
beta12orEarlier
A plot of sequence similarities identified from word-matching or character comparison.
Sequence conservation report
Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
Sequence similarity plot
beta12orEarlier
An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.
Helical wheel
beta12orEarlier
An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.
Useful for highlighting amphipathicity and other properties.
Helical net
beta12orEarlier
beta12orEarlier
A plot of general physicochemical properties of a protein sequence.
Protein sequence properties plot
true
beta12orEarlier
A plot of pK versus pH for a protein.
Protein ionisation curve
beta12orEarlier
A plot of character or word composition / frequency of a molecular sequence.
Sequence composition plot
beta12orEarlier
Density plot (of base composition) for a nucleotide sequence.
Nucleic acid density plot
beta12orEarlier
Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).
Sequence trace image
beta12orEarlier
1.5
A report on siRNA duplexes in mRNA.
Nucleic acid features (siRNA)
true
beta12orEarlier
beta12orEarlier
A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.
This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.
Sequence set (stream)
true
beta12orEarlier
Secondary identifier of an object from the FlyBase database.
Secondary identifier are used to handle entries that were merged with or split from other entries in the database.
FlyBase secondary identifier
beta12orEarlier
beta12orEarlier
The number of a certain thing.
Cardinality
true
beta12orEarlier
beta12orEarlier
A single thing.
Exactly 1
true
beta12orEarlier
beta12orEarlier
One or more things.
1 or more
true
beta12orEarlier
beta12orEarlier
Exactly two things.
Exactly 2
true
beta12orEarlier
beta12orEarlier
Two or more things.
2 or more
true
beta12orEarlier
A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.
Hash
Hash code
Hash sum
Hash value
Sequence checksum
beta12orEarlier
1.8
chemical modification of a protein.
Protein features report (chemical modifications)
true
beta12orEarlier
1.5
Data on an error generated by computer system or tool.
Error
true
beta12orEarlier
Basic information on any arbitrary database entry.
Database entry metadata
beta12orEarlier
beta13
A cluster of similar genes.
Gene cluster
true
beta12orEarlier
1.8
A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
Sequence record full
true
beta12orEarlier
true
An identifier of a plasmid in a database.
Plasmid identifier
beta12orEarlier
true
A unique identifier of a specific mutation catalogued in a database.
Mutation ID
beta12orEarlier
beta12orEarlier
Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style.
Mutation annotation (basic)
true
beta12orEarlier
beta12orEarlier
An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..
Mutation annotation (prevalence)
true
beta12orEarlier
beta12orEarlier
An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.
Mutation annotation (prognostic)
true
beta12orEarlier
beta12orEarlier
An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on.
Mutation annotation (functional)
true
beta12orEarlier
The number of a codon, for instance, at which a mutation is located.
Codon number
beta12orEarlier
1.4
An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.
Tumor annotation
true
beta12orEarlier
1.5
Basic information about a server on the web, such as an SRS server.
Server metadata
true
beta12orEarlier
The name of a field in a database.
Database field name
beta12orEarlier
Unique identifier of a sequence cluster from the SYSTERS database.
SYSTERS cluster ID
Sequence cluster ID (SYSTERS)
beta12orEarlier
Data concerning a biological ontology.
Ontology metadata
beta12orEarlier
beta13
Raw SCOP domain classification data files.
These are the parsable data files provided by SCOP.
Raw SCOP domain classification
true
beta12orEarlier
beta13
Raw CATH domain classification data files.
These are the parsable data files provided by CATH.
Raw CATH domain classification
true
beta12orEarlier
1.4
An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files.
Heterogen annotation
true
beta12orEarlier
beta12orEarlier
Phylogenetic property values data.
Phylogenetic property values
true
beta12orEarlier
1.5
A collection of sequences output from a bootstrapping (resampling) procedure.
Bootstrapping is often performed in phylogenetic analysis.
Sequence set (bootstrapped)
true
beta12orEarlier
beta12orEarlier
A consensus phylogenetic tree derived from comparison of multiple trees.
Phylogenetic consensus tree
true
beta12orEarlier
1.5
A data schema for organising or transforming data of some type.
Schema
true
beta12orEarlier
1.5
A DTD (document type definition).
DTD
true
beta12orEarlier
1.5
An XML Schema.
XML Schema
true
beta12orEarlier
1.5
A relax-NG schema.
Relax-NG schema
true
beta12orEarlier
1.5
An XSLT stylesheet.
XSLT stylesheet
true
beta12orEarlier
The name of a data type.
Data resource definition name
beta12orEarlier
Name of an OBO file format such as OBO-XML, plain and so on.
OBO file format name
beta12orEarlier
Identifier for genetic elements in MIPS database.
MIPS genetic element identifier
Gene ID (MIPS)
beta12orEarlier
beta12orEarlier
An identifier of protein sequence(s) or protein sequence database entries.
Sequence identifier (protein)
true
beta12orEarlier
beta12orEarlier
An identifier of nucleotide sequence(s) or nucleotide sequence database entries.
Sequence identifier (nucleic acid)
true
beta12orEarlier
An accession number of an entry from the EMBL sequence database.
EMBL ID
EMBL accession number
EMBL identifier
EMBL accession
beta12orEarlier
An identifier of a polypeptide in the UniProt database.
UniProt entry name
UniProt identifier
UniProtKB entry name
UniProtKB identifier
UniProt ID
beta12orEarlier
Accession number of an entry from the GenBank sequence database.
GenBank ID
GenBank accession number
GenBank identifier
GenBank accession
beta12orEarlier
Secondary (internal) identifier of a Gramene database entry.
Gramene internal ID
Gramene internal identifier
Gramene secondary ID
Gramene secondary identifier
beta12orEarlier
true
An identifier of an entry from a database of molecular sequence variation.
Sequence variation ID
beta12orEarlier
true
A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.
Gene accession
Gene code
Gene ID
beta12orEarlier
1.3
Name of an entry (gene) from the AceView genes database.
Gene name (AceView)
true
beta12orEarlier
http://www.geneontology.org/doc/GO.xrf_abbs: ECK
Identifier of an E. coli K-12 gene from EcoGene Database.
E. coli K-12 gene identifier
ECK accession
Gene ID (ECK)
beta12orEarlier
Identifier for a gene approved by the HUGO Gene Nomenclature Committee.
HGNC ID
Gene ID (HGNC)
beta12orEarlier
The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.
Allele name
Gene name
beta12orEarlier
1.3
Name of an entry (gene) from the NCBI genes database.
NCBI gene name
Gene name (NCBI)
true
beta12orEarlier
A specification of a chemical structure in SMILES format.
SMILES string
beta12orEarlier
Unique identifier of an entry from the STRING database of protein-protein interactions.
STRING ID
beta12orEarlier
1.4
An informative report on a specific virus.
Virus annotation
true
beta12orEarlier
1.4
An informative report on the taxonomy of a specific virus.
Virus annotation (taxonomy)
true
beta12orEarlier
[0-9]+
Identifier of a biological reaction from the SABIO-RK reactions database.
Reaction ID (SABIO-RK)
beta12orEarlier
A human-readable collection of information about one or more specific carbohydrate 3D structure(s).
Carbohydrate report
beta12orEarlier
A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.
NCBI GI number
Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
GI number
beta12orEarlier
An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.
NCBI accession.version
accession.version
Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.
NCBI version
beta12orEarlier
The name of a cell line.
Cell line name
beta12orEarlier
The name of a cell line.
Cell line name (exact)
beta12orEarlier
The name of a cell line.
Cell line name (truncated)
beta12orEarlier
The name of a cell line.
Cell line name (no punctuation)
beta12orEarlier
The name of a cell line.
Cell line name (assonant)
beta12orEarlier
true
A unique, persistent identifier of an enzyme.
Enzyme accession
Enzyme ID
beta12orEarlier
Identifier of an enzyme from the REBASE enzymes database.
REBASE enzyme number
beta12orEarlier
DB[0-9]{5}
Unique identifier of a drug from the DrugBank database.
DrugBank ID
beta12orEarlier
A unique identifier assigned to NCBI protein sequence records.
protein gi
protein gi number
Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
GI number (protein)
beta12orEarlier
A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system.
Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches.
Bit score
beta12orEarlier
1.20
Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.
Translation phase specification
true
beta12orEarlier
Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing.
Provenance metadata
This is a broad data type and is used a placeholder for other, more specific types.
Resource metadata
beta12orEarlier
Any arbitrary identifier of an ontology.
Ontology identifier
beta12orEarlier
The name of a concept in an ontology.
Ontology concept name
beta12orEarlier
An identifier of a build of a particular genome.
Genome build identifier
beta12orEarlier
The name of a biological pathway or network.
Pathway or network name
beta12orEarlier
[a-zA-Z_0-9]{2,3}[0-9]{5}
Identifier of a pathway from the KEGG pathway database.
KEGG pathway ID
Pathway ID (KEGG)
beta12orEarlier
[a-zA-Z_0-9]+
Identifier of a pathway from the NCI-Nature pathway database.
Pathway ID (NCI-Nature)
beta12orEarlier
Identifier of a pathway from the ConsensusPathDB pathway database.
Pathway ID (ConsensusPathDB)
beta12orEarlier
Unique identifier of an entry from the UniRef database.
UniRef cluster id
UniRef entry accession
Sequence cluster ID (UniRef)
beta12orEarlier
Unique identifier of an entry from the UniRef100 database.
UniRef100 cluster id
UniRef100 entry accession
Sequence cluster ID (UniRef100)
beta12orEarlier
Unique identifier of an entry from the UniRef90 database.
UniRef90 cluster id
UniRef90 entry accession
Sequence cluster ID (UniRef90)
beta12orEarlier
Unique identifier of an entry from the UniRef50 database.
UniRef50 cluster id
UniRef50 entry accession
Sequence cluster ID (UniRef50)
beta12orEarlier
Data concerning or derived from an ontology.
Ontological data
This is a broad data type and is used a placeholder for other, more specific types.
Ontology data
beta12orEarlier
A human-readable collection of information about a specific RNA family or other group of classified RNA sequences.
RNA family annotation
RNA family report
beta12orEarlier
true
Identifier of an RNA family, typically an entry from a RNA sequence classification database.
RNA family identifier
beta12orEarlier
Stable accession number of an entry (RNA family) from the RFAM database.
RFAM accession
beta12orEarlier
1.5
A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.
Protein signature type
true
beta12orEarlier
1.5
An informative report on protein domain-DNA/RNA interaction(s).
Domain-nucleic acid interaction report
true
beta12orEarlier
1.8
An informative report on protein domain-protein domain interaction(s).
Domain-domain interactions
true
beta12orEarlier
beta12orEarlier
Data on indirect protein domain-protein domain interaction(s).
Domain-domain interaction (indirect)
true
beta12orEarlier
true
Accession number of a nucleotide or protein sequence database entry.
Sequence accession (hybrid)
beta12orEarlier
beta13
Data concerning two-dimensional polygel electrophoresis.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
2D PAGE data
true
beta12orEarlier
1.8
two-dimensional gel electrophoresis experiments, gels or spots in a gel.
2D PAGE report
true
beta12orEarlier
true
A persistent, unique identifier of a biological pathway or network (typically a database entry).
Pathway or network accession
beta12orEarlier
Alignment of the (1D representations of) secondary structure of two or more molecules.
Secondary structure alignment
beta12orEarlier
Identifier of an object from the ASTD database.
ASTD ID
beta12orEarlier
Identifier of an exon from the ASTD database.
ASTD ID (exon)
beta12orEarlier
Identifier of an intron from the ASTD database.
ASTD ID (intron)
beta12orEarlier
Identifier of a polyA signal from the ASTD database.
ASTD ID (polya)
beta12orEarlier
Identifier of a transcription start site from the ASTD database.
ASTD ID (tss)
beta12orEarlier
1.8
An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.
2D PAGE spot report
true
beta12orEarlier
true
Unique identifier of a spot from a two-dimensional (protein) gel.
Spot ID
beta12orEarlier
Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.
Spot serial number
beta12orEarlier
Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.
Spot ID (HSC-2DPAGE)
beta12orEarlier
beta13
Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.
Protein-motif interaction
true
beta12orEarlier
true
Identifier of a strain of an organism variant, typically a plant, virus or bacterium.
Strain identifier
beta12orEarlier
A unique identifier of an item from the CABRI database.
CABRI accession
beta12orEarlier
1.8
Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.
Experiment report (genotyping)
true
beta12orEarlier
true
Identifier of an entry from a database of genotype experiment metadata.
Genotype experiment ID
beta12orEarlier
Identifier of an entry from the EGA database.
EGA accession
beta12orEarlier
IPI[0-9]{8}
Identifier of a protein entry catalogued in the International Protein Index (IPI) database.
IPI protein ID
beta12orEarlier
Accession number of a protein from the RefSeq database.
RefSeq protein ID
RefSeq accession (protein)
beta12orEarlier
Identifier of an entry (promoter) from the EPD database.
EPD identifier
EPD ID
beta12orEarlier
Identifier of an entry from the TAIR database.
TAIR accession
beta12orEarlier
Identifier of an Arabidopsis thaliana gene from the TAIR database.
TAIR accession (At gene)
beta12orEarlier
Identifier of an entry from the UniSTS database.
UniSTS accession
beta12orEarlier
Identifier of an entry from the UNITE database.
UNITE accession
beta12orEarlier
Identifier of an entry from the UTR database.
UTR accession
beta12orEarlier
UPI[A-F0-9]{10}
Accession number of a UniParc (protein sequence) database entry.
UPI
UniParc ID
UniParc accession
beta12orEarlier
Identifier of an entry from the Rouge or HUGE databases.
mFLJ/mKIAA number
beta12orEarlier
1.4
An informative report on a specific fungus.
Fungi annotation
true
beta12orEarlier
1.4
An informative report on a specific fungus anamorph.
Fungi annotation (anamorph)
true
beta12orEarlier
Unique identifier for a protein from the Ensembl database.
Ensembl ID (protein)
Protein ID (Ensembl)
Ensembl protein ID
beta12orEarlier
1.4
An informative report on a specific toxin.
Toxin annotation
true
beta12orEarlier
beta12orEarlier
An informative report on a membrane protein.
Protein report (membrane protein)
true
beta12orEarlier
1.12
An informative report on tentative or known protein-drug interaction(s).
Protein-drug interaction report
true
beta12orEarlier
beta13
Data concerning a map of molecular sequence(s).
This is a broad data type and is used a placeholder for other, more specific types.
Map data
true
beta12orEarlier
Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.
This is a broad data type and is used a placeholder for other, more specific types.
Phylogenetic data
beta12orEarlier
beta13
Data concerning one or more protein molecules.
This is a broad data type and is used a placeholder for other, more specific types.
Protein data
true
beta12orEarlier
beta13
Data concerning one or more nucleic acid molecules.
This is a broad data type and is used a placeholder for other, more specific types.
Nucleic acid data
true
beta12orEarlier
Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.
Article data
Scientific text data
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.
Text data
beta12orEarlier
1.16
Typically a simple numerical or string value that controls the operation of a tool.
Parameter
true
beta12orEarlier
beta13
Data concerning a specific type of molecule.
This is a broad data type and is used a placeholder for other, more specific types.
Molecular data
true
beta12orEarlier
1.5
An informative report on a specific molecule.
Molecule report
true
beta12orEarlier
A human-readable collection of information about a specific organism.
Organism annotation
Organism report
beta12orEarlier
A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis.
Experiment annotation
Experiment metadata
Experiment report
Protocol
beta12orEarlier
An attribute of a molecular sequence, possibly in reference to some other sequence.
Sequence parameter
Sequence attribute
beta12orEarlier
Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed.
Sequencing-based expression profile
Sequence tag profile (with gene assignment)
SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.
This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.
Sequence tag profile
beta12orEarlier
Data concerning a mass spectrometry measurement.
Mass spectrometry data
beta12orEarlier
Raw data from experimental methods for determining protein structure.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Protein structure raw data
beta12orEarlier
true
An identifier of a mutation.
Mutation identifier
beta12orEarlier
beta13
Data concerning an alignment of two or more molecular sequences, structures or derived data.
This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles.
Alignment data
true
beta12orEarlier
beta13
Data concerning an index of data.
This is a broad data type and is used a placeholder for other, more specific types.
Data index data
true
beta12orEarlier
Single letter amino acid identifier, e.g. G.
Amino acid name (single letter)
beta12orEarlier
Three letter amino acid identifier, e.g. GLY.
Amino acid name (three letter)
beta12orEarlier
Full name of an amino acid, e.g. Glycine.
Amino acid name (full name)
beta12orEarlier
true
Identifier of a toxin.
Toxin identifier
beta12orEarlier
Unique identifier of a toxin from the ArachnoServer database.
ArachnoServer ID
beta12orEarlier
1.5
A simple summary of expressed genes.
Expressed gene list
true
beta12orEarlier
Unique identifier of a monomer from the BindingDB database.
BindingDB Monomer ID
beta12orEarlier
beta12orEarlier
The name of a concept from the GO ontology.
GO concept name
true
beta12orEarlier
[0-9]{7}|GO:[0-9]{7}
An identifier of a 'biological process' concept from the the Gene Ontology.
GO concept ID (biological process)
beta12orEarlier
[0-9]{7}|GO:[0-9]{7}
An identifier of a 'molecular function' concept from the the Gene Ontology.
GO concept ID (molecular function)
beta12orEarlier
beta12orEarlier
The name of a concept for a cellular component from the GO ontology.
GO concept name (cellular component)
true
beta12orEarlier
An image arising from a Northern Blot experiment.
Northern blot image
beta12orEarlier
true
Unique identifier of a blot from a Northern Blot.
Blot ID
beta12orEarlier
Unique identifier of a blot from a Northern Blot from the BlotBase database.
BlotBase blot ID
beta12orEarlier
Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.
Hierarchy annotation
Hierarchy
beta12orEarlier
beta12orEarlier
Identifier of an entry from a database of biological hierarchies.
Hierarchy identifier
true
beta12orEarlier
Identifier of an entry from the Brite database of biological hierarchies.
Brite hierarchy ID
beta12orEarlier
beta12orEarlier
A type (represented as a string) of cancer.
Cancer type
true
beta12orEarlier
A unique identifier for an organism used in the BRENDA database.
BRENDA organism ID
beta12orEarlier
The name of a taxon using the controlled vocabulary of the UniGene database.
UniGene organism abbreviation
UniGene taxon
beta12orEarlier
The name of a taxon using the controlled vocabulary of the UTRdb database.
UTRdb taxon
beta12orEarlier
true
An identifier of a catalogue of biological resources.
Catalogue identifier
Catalogue ID
beta12orEarlier
The name of a catalogue of biological resources from the CABRI database.
CABRI catalogue name
beta12orEarlier
beta12orEarlier
An informative report on protein secondary structure alignment-derived data or metadata.
Secondary structure alignment metadata
true
beta12orEarlier
Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19.
1.5
An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).
Molecule interaction report
true
beta12orEarlier
Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).
Network
Pathway
Pathway or network
beta12orEarlier
beta13
Data concerning one or more small molecules.
This is a broad data type and is used a placeholder for other, more specific types.
Small molecule data
true
beta12orEarlier
beta13
Data concerning a particular genotype, phenotype or a genotype / phenotype relation.
Genotype and phenotype data
true
beta12orEarlier
Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification.
Gene expression data
Gene product profile
Gene product quantification data
Gene transcription profile
Gene transcription quantification data
Metabolite expression data
Microarray data
Non-coding RNA profile
Non-coding RNA quantification data
Protein expression data
RNA profile
RNA quantification data
RNA-seq data
Transcriptome profile
Transcriptome quantification data
mRNA profile
mRNA quantification data
Protein profile
Protein quantification data
Proteome profile
Proteome quantification data
Expression data
beta12orEarlier
C[0-9]+
Unique identifier of a chemical compound from the KEGG database.
KEGG compound ID
KEGG compound identifier
Compound ID (KEGG)
beta12orEarlier
Name (not necessarily stable) an entry (RNA family) from the RFAM database.
RFAM name
beta12orEarlier
R[0-9]+
Identifier of a biological reaction from the KEGG reactions database.
Reaction ID (KEGG)
beta12orEarlier
D[0-9]+
Unique identifier of a drug from the KEGG Drug database.
Drug ID (KEGG)
beta12orEarlier
ENS[A-Z]*[FPTG][0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.
Ensembl IDs
Ensembl ID
beta12orEarlier
[A-Z][0-9]+(\.[-[0-9]+])?
An identifier of a disease from the International Classification of Diseases (ICD) database.
ICD identifier
beta12orEarlier
[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?
Unique identifier of a sequence cluster from the CluSTr database.
CluSTr ID
CluSTr cluster ID
Sequence cluster ID (CluSTr)
beta12orEarlier
G[0-9]+
Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).
KEGG Glycan ID
beta12orEarlier
[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+
A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.
TC number
OBO file for regular expression.
TCDB ID
beta12orEarlier
MINT\-[0-9]{1,5}
Unique identifier of an entry from the MINT database of protein-protein interactions.
MINT ID
beta12orEarlier
DIP[\:\-][0-9]{3}[EN]
Unique identifier of an entry from the DIP database of protein-protein interactions.
DIP ID
beta12orEarlier
A[0-9]{6}
Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.
Signaling Gateway protein ID
beta12orEarlier
true
Identifier of a protein modification catalogued in a database.
Protein modification ID
beta12orEarlier
AA[0-9]{4}
Identifier of a protein modification catalogued in the RESID database.
RESID ID
beta12orEarlier
[0-9]{4,7}
Identifier of an entry from the RGD database.
RGD ID
beta12orEarlier
AASequence:[0-9]{10}
Identifier of a protein sequence from the TAIR database.
TAIR accession (protein)
beta12orEarlier
HMDB[0-9]{5}
Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).
HMDB ID
Compound ID (HMDB)
beta12orEarlier
LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?
Identifier of an entry from the LIPID MAPS database.
LM ID
LIPID MAPS ID
beta12orEarlier
PAp[0-9]{8}
PDBML:pdbx_PDB_strand_id
Identifier of a peptide from the PeptideAtlas peptide databases.
PeptideAtlas ID
beta12orEarlier
1.7
Identifier of a report of molecular interactions from a database (typically).
Molecular interaction ID
true
beta12orEarlier
[0-9]+
A unique identifier of an interaction from the BioGRID database.
BioGRID interaction ID
beta12orEarlier
S[0-9]{2}\.[0-9]{3}
Unique identifier of a peptidase enzyme from the MEROPS database.
MEROPS ID
Enzyme ID (MEROPS)
beta12orEarlier
true
An identifier of a mobile genetic element.
Mobile genetic element ID
beta12orEarlier
mge:[0-9]+
An identifier of a mobile genetic element from the Aclame database.
ACLAME ID
beta12orEarlier
PWY[a-zA-Z_0-9]{2}\-[0-9]{3}
Identifier of an entry from the Saccharomyces genome database (SGD).
SGD ID
beta12orEarlier
true
Unique identifier of a book.
Book ID
beta12orEarlier
(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)
The International Standard Book Number (ISBN) is for identifying printed books.
ISBN
beta12orEarlier
B[0-9]{5}
Identifier of a metabolite from the 3DMET database.
3DMET ID
Compound ID (3DMET)
beta12orEarlier
([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)
A unique identifier of an interaction from the MatrixDB database.
MatrixDB interaction ID
beta12orEarlier
[0-9]+
A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.
These identifiers are unique within the cPath database, however, they are not stable between releases.
cPath ID
beta12orEarlier
true
[0-9]+
Identifier of an assay from the PubChem database.
PubChem bioassay ID
beta12orEarlier
Identifier of an entry from the PubChem database.
PubChem identifier
PubChem ID
beta12orEarlier
M[0-9]{4}
Identifier of an enzyme reaction mechanism from the MACie database.
MACie entry number
Reaction ID (MACie)
beta12orEarlier
MI[0-9]{7}
Identifier for a gene from the miRBase database.
miRNA ID
miRNA identifier
miRNA name
Gene ID (miRBase)
beta12orEarlier
ZDB\-GENE\-[0-9]+\-[0-9]+
Identifier for a gene from the Zebrafish information network genome (ZFIN) database.
Gene ID (ZFIN)
beta12orEarlier
[0-9]{5}
Identifier of an enzyme-catalysed reaction from the Rhea database.
Reaction ID (Rhea)
beta12orEarlier
UPA[0-9]{5}
Identifier of a biological pathway from the Unipathway database.
upaid
Pathway ID (Unipathway)
beta12orEarlier
[0-9]+
Identifier of a small molecular from the ChEMBL database.
ChEMBL ID
Compound ID (ChEMBL)
beta12orEarlier
[a-zA-Z_0-9]+
Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.
LGICdb identifier
beta12orEarlier
[0-9]+
Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.
Reaction kinetics ID (SABIO-RK)
beta12orEarlier
PA[0-9]+
Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
PharmGKB ID
beta12orEarlier
PA[0-9]+
Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Pathway ID (PharmGKB)
beta12orEarlier
PA[0-9]+
Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Disease ID (PharmGKB)
beta12orEarlier
PA[0-9]+
Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Drug ID (PharmGKB)
beta12orEarlier
DAP[0-9]+
Identifier of a drug from the Therapeutic Target Database (TTD).
Drug ID (TTD)
beta12orEarlier
TTDS[0-9]+
Identifier of a target protein from the Therapeutic Target Database (TTD).
Target ID (TTD)
beta12orEarlier
true
A unique identifier of a type or group of cells.
Cell type identifier
beta12orEarlier
[0-9]+
A unique identifier of a neuron from the NeuronDB database.
NeuronDB ID
beta12orEarlier
[a-zA-Z_0-9]+
A unique identifier of a neuron from the NeuroMorpho database.
NeuroMorpho ID
beta12orEarlier
[0-9]+
Identifier of a chemical from the ChemIDplus database.
ChemIDplus ID
Compound ID (ChemIDplus)
beta12orEarlier
SMP[0-9]{5}
Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).
Pathway ID (SMPDB)
beta12orEarlier
[0-9]+
Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.
BioNumbers ID
beta12orEarlier
T3D[0-9]+
Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.
T3DB ID
beta12orEarlier
true
Identifier of a carbohydrate.
Carbohydrate identifier
beta12orEarlier
[0-9]+
Identifier of an entry from the GlycomeDB database.
GlycomeDB ID
beta12orEarlier
[a-zA-Z_0-9]+[0-9]+
Identifier of an entry from the LipidBank database.
LipidBank ID
beta12orEarlier
cd[0-9]{5}
Identifier of a conserved domain from the Conserved Domain Database.
CDD ID
beta12orEarlier
[0-9]{1,5}
An identifier of an entry from the MMDB database.
MMDB accession
MMDB ID
beta12orEarlier
[0-9]+
Unique identifier of an entry from the iRefIndex database of protein-protein interactions.
iRefIndex ID
beta12orEarlier
[0-9]+
Unique identifier of an entry from the ModelDB database.
ModelDB ID
beta12orEarlier
[0-9]+
Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).
Pathway ID (DQCS)
beta12orEarlier
beta12orEarlier
ENS([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division).
Ensembl ID (Homo sapiens)
true
beta12orEarlier
beta12orEarlier
ENSBTA([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division).
Ensembl ID ('Bos taurus')
true
beta12orEarlier
beta12orEarlier
ENSCAF([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division).
Ensembl ID ('Canis familiaris')
true
beta12orEarlier
beta12orEarlier
ENSCPO([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division).
Ensembl ID ('Cavia porcellus')
true
beta12orEarlier
beta12orEarlier
ENSCIN([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division).
Ensembl ID ('Ciona intestinalis')
true
beta12orEarlier
beta12orEarlier
ENSCSAV([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division).
Ensembl ID ('Ciona savignyi')
true
beta12orEarlier
beta12orEarlier
ENSDAR([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division).
Ensembl ID ('Danio rerio')
true
beta12orEarlier
beta12orEarlier
ENSDNO([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division).
Ensembl ID ('Dasypus novemcinctus')
true
beta12orEarlier
beta12orEarlier
ENSETE([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division).
Ensembl ID ('Echinops telfairi')
true
beta12orEarlier
beta12orEarlier
ENSEEU([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division).
Ensembl ID ('Erinaceus europaeus')
true
beta12orEarlier
beta12orEarlier
ENSFCA([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division).
Ensembl ID ('Felis catus')
true
beta12orEarlier
beta12orEarlier
ENSGAL([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division).
Ensembl ID ('Gallus gallus')
true
beta12orEarlier
beta12orEarlier
ENSGAC([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division).
Ensembl ID ('Gasterosteus aculeatus')
true
beta12orEarlier
beta12orEarlier
ENSHUM([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division).
Ensembl ID ('Homo sapiens')
true
beta12orEarlier
beta12orEarlier
ENSLAF([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division).
Ensembl ID ('Loxodonta africana')
true
beta12orEarlier
beta12orEarlier
ENSMMU([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division).
Ensembl ID ('Macaca mulatta')
true
beta12orEarlier
beta12orEarlier
ENSMOD([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division).
Ensembl ID ('Monodelphis domestica')
true
beta12orEarlier
beta12orEarlier
ENSMUS([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division).
Ensembl ID ('Mus musculus')
true
beta12orEarlier
beta12orEarlier
ENSMLU([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division).
Ensembl ID ('Myotis lucifugus')
true
beta12orEarlier
beta12orEarlier
ENSOAN([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division).
Ensembl ID ("Ornithorhynchus anatinus")
true
beta12orEarlier
beta12orEarlier
ENSOCU([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division).
Ensembl ID ('Oryctolagus cuniculus')
true
beta12orEarlier
beta12orEarlier
ENSORL([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division).
Ensembl ID ('Oryzias latipes')
true
beta12orEarlier
beta12orEarlier
ENSSAR([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division).
Ensembl ID ('Otolemur garnettii')
true
beta12orEarlier
beta12orEarlier
ENSPTR([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division).
Ensembl ID ('Pan troglodytes')
true
beta12orEarlier
beta12orEarlier
ENSRNO([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division).
Ensembl ID ('Rattus norvegicus')
true
beta12orEarlier
beta12orEarlier
ENSSTO([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division).
Ensembl ID ('Spermophilus tridecemlineatus')
true
beta12orEarlier
beta12orEarlier
ENSFRU([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division).
Ensembl ID ('Takifugu rubripes')
true
beta12orEarlier
beta12orEarlier
ENSTBE([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division).
Ensembl ID ('Tupaia belangeri')
true
beta12orEarlier
beta12orEarlier
ENSXET([EGTP])[0-9]{11}
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division).
Ensembl ID ('Xenopus tropicalis')
true
beta12orEarlier
Identifier of a protein domain (or other node) from the CATH database.
CATH identifier
beta12orEarlier
2.10.10.10
A code number identifying a family from the CATH database.
CATH node ID (family)
beta12orEarlier
Identifier of an enzyme from the CAZy enzymes database.
CAZy ID
Enzyme ID (CAZy)
beta12orEarlier
A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).
I.M.A.G.E. cloneID
IMAGE cloneID
Clone ID (IMAGE)
beta12orEarlier
[0-9]{7}|GO:[0-9]{7}
An identifier of a 'cellular component' concept from the Gene Ontology.
GO concept identifier (cellular compartment)
GO concept ID (cellular component)
beta12orEarlier
Name of a chromosome as used in the BioCyc database.
Chromosome name (BioCyc)
beta12orEarlier
An identifier of a gene expression profile from the CleanEx database.
CleanEx entry name
beta12orEarlier
An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.
CleanEx dataset code
beta12orEarlier
A human-readable collection of information concerning a genome as a whole.
Genome report
beta12orEarlier
Unique identifier for a protein complex from the CORUM database.
CORUM complex ID
Protein ID (CORUM)
beta12orEarlier
Unique identifier of a position-specific scoring matrix from the CDD database.
CDD PSSM-ID
beta12orEarlier
Unique identifier for a protein from the CuticleDB database.
CuticleDB ID
Protein ID (CuticleDB)
beta12orEarlier
Identifier of a predicted transcription factor from the DBD database.
DBD ID
beta12orEarlier
General annotation on an oligonucleotide probe, or a set of probes.
Oligonucleotide probe sets annotation
Oligonucleotide probe annotation
beta12orEarlier
true
Identifier of an oligonucleotide from a database.
Oligonucleotide ID
beta12orEarlier
Identifier of an oligonucleotide probe from the dbProbe database.
dbProbe ID
beta12orEarlier
Physicochemical property data for one or more dinucleotides.
Dinucleotide property
beta12orEarlier
Identifier of an dinucleotide property from the DiProDB database.
DiProDB ID
beta12orEarlier
1.8
disordered structure in a protein.
Protein features report (disordered structure)
true
beta12orEarlier
Unique identifier for a protein from the DisProt database.
DisProt ID
Protein ID (DisProt)
beta12orEarlier
1.5
Annotation on an embryo or concerning embryological development.
Embryo report
true
beta12orEarlier
Unique identifier for a gene transcript from the Ensembl database.
Transcript ID (Ensembl)
Ensembl transcript ID
beta12orEarlier
1.4
An informative report on one or more small molecules that are enzyme inhibitors.
Inhibitor annotation
true
beta12orEarlier
true
Moby:GeneAccessionList
An identifier of a promoter of a gene that is catalogued in a database.
Promoter ID
beta12orEarlier
Identifier of an EST sequence.
EST accession
beta12orEarlier
Identifier of an EST sequence from the COGEME database.
COGEME EST ID
beta12orEarlier
Identifier of a unisequence from the COGEME database.
A unisequence is a single sequence assembled from ESTs.
COGEME unisequence ID
beta12orEarlier
Accession number of an entry (family) from the TIGRFam database.
GeneFarm family ID
Protein family ID (GeneFarm)
beta12orEarlier
The name of a family of organism.
Family name
beta12orEarlier
beta13
The name of a genus of viruses.
Genus name (virus)
true
beta12orEarlier
beta13
The name of a family of viruses.
Family name (virus)
true
beta12orEarlier
beta13
The name of a SwissRegulon database.
Database name (SwissRegulon)
true
beta12orEarlier
A feature identifier as used in the SwissRegulon database.
This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".
Sequence feature ID (SwissRegulon)
beta12orEarlier
A unique identifier of gene in the NMPDR database.
A FIG ID consists of four parts: a prefix, genome id, locus type and id number.
FIG ID
beta12orEarlier
A unique identifier of gene in the Xenbase database.
Gene ID (Xenbase)
beta12orEarlier
A unique identifier of gene in the Genolist database.
Gene ID (Genolist)
beta12orEarlier
1.3
Name of an entry (gene) from the Genolist genes database.
Genolist gene name
Gene name (Genolist)
true
beta12orEarlier
Identifier of an entry (promoter) from the ABS database.
ABS identifier
ABS ID
beta12orEarlier
Identifier of a transcription factor from the AraC-XylS database.
AraC-XylS ID
beta12orEarlier
beta12orEarlier
Name of an entry (gene) from the HUGO database.
Gene name (HUGO)
true
beta12orEarlier
Identifier of a locus from the PseudoCAP database.
Locus ID (PseudoCAP)
beta12orEarlier
Identifier of a locus from the UTR database.
Locus ID (UTR)
beta12orEarlier
Unique identifier of a monosaccharide from the MonosaccharideDB database.
MonosaccharideDB ID
beta12orEarlier
beta13
The name of a subdivision of the Collagen Mutation Database (CMD) database.
Database name (CMD)
true
beta12orEarlier
beta13
The name of a subdivision of the Osteogenesis database.
Database name (Osteogenesis)
true
beta12orEarlier
true
An identifier of a particular genome.
Genome identifier
beta12orEarlier
An identifier of a particular genome.
GenomeReviews ID
beta12orEarlier
[0-9]+
Identifier of an entry from the GlycosciencesDB database.
GlycoMap ID
beta12orEarlier
A conformational energy map of the glycosidic linkages in a carbohydrate molecule.
Carbohydrate conformational map
beta12orEarlier
The name of a transcription factor.
Transcription factor name
beta12orEarlier
Identifier of a membrane transport proteins from the transport classification database (TCDB).
TCID
beta12orEarlier
PF[0-9]{5}
Name of a domain from the Pfam database.
Pfam domain name
beta12orEarlier
CL[0-9]{4}
Accession number of a Pfam clan.
Pfam clan ID
beta12orEarlier
Identifier for a gene from the VectorBase database.
VectorBase ID
Gene ID (VectorBase)
beta12orEarlier
Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.
UTRSite ID
beta12orEarlier
An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.
Sequence motif report
Sequence profile report
Sequence signature report
beta12orEarlier
beta12orEarlier
An informative report on a particular locus.
Locus report
Locus annotation
true
beta12orEarlier
Official name of a protein as used in the UniProt database.
Protein name (UniProt)
beta12orEarlier
1.5
One or more terms from one or more controlled vocabularies which are annotations on an entity.
The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.
Term ID list
true
beta12orEarlier
Name of a protein family from the HAMAP database.
HAMAP ID
beta12orEarlier
1.12
Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance.
Identifier with metadata
true
beta12orEarlier
beta12orEarlier
Annotation about a gene symbol.
Gene symbol annotation
true
beta12orEarlier
true
Identifier of a RNA transcript.
Transcript ID
beta12orEarlier
Identifier of an RNA transcript from the H-InvDB database.
HIT ID
beta12orEarlier
A unique identifier of gene cluster in the H-InvDB database.
HIX ID
beta12orEarlier
Identifier of a antibody from the HPA database.
HPA antibody id
beta12orEarlier
Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.
IMGT/HLA ID
beta12orEarlier
A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).
Gene ID (JCVI)
beta12orEarlier
The name of a kinase protein.
Kinase name
beta12orEarlier
Identifier of a physical entity from the ConsensusPathDB database.
ConsensusPathDB entity ID
beta12orEarlier
Name of a physical entity from the ConsensusPathDB database.
ConsensusPathDB entity name
beta12orEarlier
The number of a strain of algae and protozoa from the CCAP database.
CCAP strain number
beta12orEarlier
true
An identifier of stock from a catalogue of biological resources.
Stock number
beta12orEarlier
A stock number from The Arabidopsis information resource (TAIR).
Stock number (TAIR)
beta12orEarlier
Identifier of an entry from the RNA editing database (REDIdb).
REDIdb ID
beta12orEarlier
Name of a domain from the SMART database.
SMART domain name
beta12orEarlier
Accession number of an entry (family) from the PANTHER database.
Panther family ID
Protein family ID (PANTHER)
beta12orEarlier
A unique identifier for a virus from the RNAVirusDB database.
Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
RNAVirusDB ID
beta12orEarlier
true
An accession of annotation on a (group of) viruses (catalogued in a database).
Virus ID
beta12orEarlier
An identifier of a genome project assigned by NCBI.
NCBI Genome Project ID
beta12orEarlier
A unique identifier of a whole genome assigned by the NCBI.
NCBI genome accession
beta12orEarlier
1.8
Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on.
Sequence profile data
true
beta12orEarlier
Unique identifier for a membrane protein from the TopDB database.
TopDB ID
Protein ID (TopDB)
beta12orEarlier
true
Identifier of a two-dimensional (protein) gel.
Gel identifier
Gel ID
beta12orEarlier
Name of a reference map gel from the SWISS-2DPAGE database.
Reference map name (SWISS-2DPAGE)
beta12orEarlier
Unique identifier for a peroxidase protein from the PeroxiBase database.
PeroxiBase ID
Protein ID (PeroxiBase)
beta12orEarlier
Identifier of an entry from the SISYPHUS database of tertiary structure alignments.
SISYPHUS ID
beta12orEarlier
true
Accession of an open reading frame (catalogued in a database).
ORF ID
beta12orEarlier
true
An identifier of an open reading frame.
ORF identifier
beta12orEarlier
Identifier of an entry from the GlycosciencesDB database.
Linucs ID
beta12orEarlier
Unique identifier for a ligand-gated ion channel protein from the LGICdb database.
LGICdb ID
Protein ID (LGICdb)
beta12orEarlier
Identifier of an EST sequence from the MaizeDB database.
MaizeDB ID
beta12orEarlier
A unique identifier of gene in the MfunGD database.
Gene ID (MfunGD)
beta12orEarlier
An identifier of a disease from the Orpha database.
Orpha number
beta12orEarlier
Unique identifier for a protein from the EcID database.
Protein ID (EcID)
beta12orEarlier
A unique identifier of a cDNA molecule catalogued in the RefSeq database.
Clone ID (RefSeq)
beta12orEarlier
Unique identifier for a cone snail toxin protein from the ConoServer database.
Protein ID (ConoServer)
beta12orEarlier
Identifier of a GeneSNP database entry.
GeneSNP ID
beta12orEarlier
true
Identifier of a lipid.
Lipid identifier
beta12orEarlier
beta12orEarlier
A flat-file (textual) data archive.
Databank
true
beta12orEarlier
beta12orEarlier
A web site providing data (web pages) on a common theme to a HTTP client.
Web portal
true
beta12orEarlier
Identifier for a gene from the VBASE2 database.
VBASE2 ID
Gene ID (VBASE2)
beta12orEarlier
A unique identifier for a virus from the DPVweb database.
DPVweb virus ID
DPVweb ID
beta12orEarlier
[0-9]+
Identifier of a pathway from the BioSystems pathway database.
Pathway ID (BioSystems)
beta12orEarlier
beta12orEarlier
Data concerning a proteomics experiment.
Experimental data (proteomics)
true
beta12orEarlier
An abstract of a scientific article.
Abstract
beta12orEarlier
3D coordinate and associated data for a lipid structure.
Lipid structure
beta12orEarlier
3D coordinate and associated data for the (3D) structure of a drug.
Drug structure
beta12orEarlier
3D coordinate and associated data for the (3D) structure of a toxin.
Toxin structure
beta12orEarlier
A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.
PSSM
Position-specific scoring matrix
beta12orEarlier
A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.
Distance matrix
beta12orEarlier
Distances (values representing similarity) between a group of molecular structures.
Structural distance matrix
beta12orEarlier
1.5
Bibliographic data concerning scientific article(s).
Article metadata
true
beta12orEarlier
A concept from a biological ontology.
This includes any fields from the concept definition such as concept name, definition, comments and so on.
Ontology concept
beta12orEarlier
A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.
Codon usage bias
beta12orEarlier
1.8
Northern Blot experiments.
Northern blot report
true
beta12orEarlier
A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.
RH map
The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.
Radiation hybrid map
beta12orEarlier
A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.
ID list
beta12orEarlier
Gene frequencies data that may be read during phylogenetic tree calculation.
Phylogenetic gene frequencies data
beta12orEarlier
beta13
A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.
Sequence set (polymorphic)
true
beta12orEarlier
1.5
An entry (resource) from the DRCAT bioinformatics resource catalogue.
DRCAT resource
true
beta12orEarlier
3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.
Protein complex
beta12orEarlier
3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role.
Protein structural motif
beta12orEarlier
A human-readable collection of information about one or more specific lipid 3D structure(s).
Lipid report
beta12orEarlier
1.4
Image of one or more molecular secondary structures.
Secondary structure image
true
beta12orEarlier
1.5
An informative report on general information, properties or features of one or more molecular secondary structures.
Secondary structure report
true
beta12orEarlier
beta12orEarlier
DNA sequence-specific feature annotation (not in a feature table).
DNA features
true
beta12orEarlier
1.5
Features concerning RNA or regions of DNA that encode an RNA molecule.
RNA features report
true
beta12orEarlier
Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph.
Graph data
Plot
beta12orEarlier
A protein sequence and associated metadata.
Sequence record (protein)
Protein sequence record
beta12orEarlier
A nucleic acid sequence and associated metadata.
Nucleotide sequence record
Sequence record (nucleic acid)
DNA sequence record
RNA sequence record
Nucleic acid sequence record
beta12orEarlier
1.8
A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
Protein sequence record (full)
true
beta12orEarlier
1.8
A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
Nucleic acid sequence record (full)
true
beta12orEarlier
true
Accession of a mathematical model, typically an entry from a database.
Biological model accession
beta12orEarlier
The name of a type or group of cells.
Cell type name
beta12orEarlier
true
Accession of a type or group of cells (catalogued in a database).
Cell type ID
Cell type accession
beta12orEarlier
true
Accession of an entry from a database of chemicals.
Chemical compound accession
Small molecule accession
Compound accession
beta12orEarlier
true
Accession of a drug.
Drug accession
beta12orEarlier
Name of a toxin.
Toxin name
beta12orEarlier
true
Accession of a toxin (catalogued in a database).
Toxin accession
beta12orEarlier
true
Accession of a monosaccharide (catalogued in a database).
Monosaccharide accession
beta12orEarlier
Common name of a drug.
Drug name
beta12orEarlier
true
Accession of an entry from a database of carbohydrates.
Carbohydrate accession
beta12orEarlier
true
Accession of a specific molecule (catalogued in a database).
Molecule accession
beta12orEarlier
true
Accession of a data definition (catalogued in a database).
Data resource definition accession
beta12orEarlier
true
An accession of a particular genome (in a database).
Genome accession
beta12orEarlier
true
An accession of a map of a molecular sequence (deposited in a database).
Map accession
beta12orEarlier
true
Accession of an entry from a database of lipids.
Lipid accession
beta12orEarlier
true
Accession of a peptide deposited in a database.
Peptide ID
beta12orEarlier
true
Accession of a protein deposited in a database.
Protein accessions
Protein accession
beta12orEarlier
true
An accession of annotation on a (group of) organisms (catalogued in a database).
Organism accession
beta12orEarlier
Moby:BriefOccurrenceRecord
Moby:FirstEpithet
Moby:InfraspecificEpithet
Moby:OccurrenceRecord
Moby:Organism_Name
Moby:OrganismsLongName
Moby:OrganismsShortName
The name of an organism (or group of organisms).
Organism name
beta12orEarlier
true
Accession of a protein family (that is deposited in a database).
Protein family accession
beta12orEarlier
true
Accession of an entry from a database of transcription factors or binding sites.
Transcription factor accession
beta12orEarlier
true
Identifier of a strain of an organism variant, typically a plant, virus or bacterium.
Strain accession
beta12orEarlier
true
An accession of annotation on a (group of) viruses (catalogued in a database).
Virus identifier
beta12orEarlier
Metadata on sequence features.
Sequence features metadata
beta12orEarlier
Identifier of a Gramene database entry.
Gramene identifier
beta12orEarlier
An identifier of an entry from the DDBJ sequence database.
DDBJ ID
DDBJ accession number
DDBJ identifier
DDBJ accession
beta12orEarlier
An identifier of an entity from the ConsensusPathDB database.
ConsensusPathDB identifier
beta12orEarlier
1.8
Data concerning, extracted from, or derived from the analysis of molecular sequence(s).
This is a broad data type and is used a placeholder for other, more specific types.
Sequence data
true
beta12orEarlier
beta13
Data concerning codon usage.
This is a broad data type and is used a placeholder for other, more specific types.
Codon usage
true
beta12orEarlier
1.5
Data derived from the analysis of a scientific text such as a full text article from a scientific journal.
Article report
true
beta12orEarlier
An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.
Sequence-derived report
Sequence report
beta12orEarlier
Data concerning the properties or features of one or more protein secondary structures.
Protein secondary structure
beta12orEarlier
A Hopp and Woods plot of predicted antigenicity of a peptide or protein.
Hopp and Woods plot
beta12orEarlier
1.21
A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
Nucleic acid melting curve
true
beta12orEarlier
1.21
A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
Nucleic acid probability profile
true
beta12orEarlier
1.21
A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
Nucleic acid temperature profile
true
beta12orEarlier
1.8
A report typically including a map (diagram) of a gene regulatory network.
Gene regulatory network report
true
beta12orEarlier
1.8
An informative report on a two-dimensional (2D PAGE) gel.
2D PAGE gel report
true
beta12orEarlier
1.14
General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set.
Oligonucleotide probe sets annotation
true
beta12orEarlier
1.5
An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.
Microarray image
true
beta12orEarlier
Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen.
Image data
Image
http://semanticscience.org/resource/SIO_000079
http://semanticscience.org/resource/SIO_000081
beta12orEarlier
Image of a molecular sequence, possibly with sequence features or properties shown.
Sequence image
beta12orEarlier
A report on protein properties concerning hydropathy.
Protein hydropathy report
Protein hydropathy data
beta12orEarlier
beta13
Data concerning a computational workflow.
Workflow data
true
beta12orEarlier
1.5
A computational workflow.
Workflow
true
beta12orEarlier
beta13
Data concerning molecular secondary structure data.
Secondary structure data
true
beta12orEarlier
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
1.23
A raw protein sequence (string of characters).
Raw amino acid sequence
Raw amino acid sequences
Raw protein sequence
Raw sequence (protein)
Protein sequence (raw)
true
beta12orEarlier
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
1.23
A raw nucleic acid sequence.
Nucleic acid raw sequence
Nucleotide sequence (raw)
Raw nucleic acid sequence
Raw sequence (nucleic acid)
Nucleic acid sequence (raw)
true
beta12orEarlier
One or more protein sequences, possibly with associated annotation.
Amino acid sequence
Amino acid sequences
Protein sequences
Protein sequence
http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation
beta12orEarlier
One or more nucleic acid sequences, possibly with associated annotation.
Nucleic acid sequences
Nucleotide sequence
Nucleotide sequences
DNA sequence
Nucleic acid sequence
http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation
beta12orEarlier
Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.
Enzyme kinetics annotation
Reaction annotation
This is a broad data type and is used a placeholder for other, more specific types.
Reaction data
beta12orEarlier
Data concerning small peptides.
Peptide data
Peptide property
beta12orEarlier
Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19.
1.5
An informative report concerning the classification of protein sequences or structures.
This is a broad data type and is used a placeholder for other, more specific types.
Protein classification
true
beta12orEarlier
1.8
Data concerning specific or conserved pattern in molecular sequences.
This is a broad data type and is used a placeholder for other, more specific types.
Sequence motif data
true
beta12orEarlier
beta13
Data concerning models representing a (typically multiple) sequence alignment.
This is a broad data type and is used a placeholder for other, more specific types.
Sequence profile data
true
beta12orEarlier
beta13
Data concerning a specific biological pathway or network.
Pathway or network data
true
beta12orEarlier
An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.
Pathway or network report
beta12orEarlier
A thermodynamic or kinetic property of a nucleic acid molecule.
Nucleic acid property (thermodynamic or kinetic)
Nucleic acid thermodynamic property
Nucleic acid thermodynamic data
beta12orEarlier
Was deprecated since 1.5, but not correctly (fully) obsoleted until 1.19.
1.5
Data concerning the classification of nucleic acid sequences or structures.
This is a broad data type and is used a placeholder for other, more specific types.
Nucleic acid classification
true
beta12orEarlier
1.5
A report on a classification of molecular sequences, structures or other entities.
This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.
Classification report
true
beta12orEarlier
1.8
key residues involved in protein folding.
Protein features report (key folding sites)
true
beta12orEarlier
Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc.
Torsion angle data
Protein geometry data
beta12orEarlier
An image of protein structure.
Structure image (protein)
Protein structure image
beta12orEarlier
Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.
Phylogenetic character weights
beta12orEarlier
Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.
Genome annotation track
Genome track
Genome-browser track
Genomic track
Sequence annotation track
Annotation track
beta12orEarlier
P43353|Q7M1G0|Q9C199|A5A6J6
[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}
Accession number of a UniProt (protein sequence) database entry.
UniProt accession number
UniProt entry accession
UniProtKB accession
UniProtKB accession number
Swiss-Prot entry accession
TrEMBL entry accession
UniProt accession
beta12orEarlier
16
[1-9][0-9]?
Identifier of a genetic code in the NCBI list of genetic codes.
NCBI genetic code ID
beta12orEarlier
Identifier of a concept in an ontology of biological or bioinformatics concepts and relations.
Ontology concept identifier
beta12orEarlier
beta12orEarlier
The name of a concept for a biological process from the GO ontology.
GO concept name (biological process)
true
beta12orEarlier
beta12orEarlier
The name of a concept for a molecular function from the GO ontology.
GO concept name (molecular function)
true
beta12orEarlier
Data concerning the classification, identification and naming of organisms.
Taxonomic data
This is a broad data type and is used a placeholder for other, more specific types.
Taxonomy
beta13
EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.
This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.
Protein ID (EMBL/GenBank/DDBJ)
beta13
1.5
A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation.
Core data entities typically have a format and may be identified by an accession number.
Core data
true
beta13
true
Name or other identifier of molecular sequence feature(s).
Sequence feature identifier
beta13
true
An identifier of a molecular tertiary structure, typically an entry from a structure database.
Structure identifier
beta13
true
An identifier of an array of numerical values, such as a comparison matrix.
Matrix identifier
beta13
1.8
A report (typically a table) on character or word composition / frequency of protein sequence(s).
Protein sequence composition
true
beta13
1.8
A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).
Nucleic acid sequence composition (report)
true
beta13
1.5
A node from a classification of protein structural domain(s).
Protein domain classification node
true
beta13
Duplicates http://edamontology.org/data_1002, hence deprecated.
1.23
Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.
CAS number
true
beta13
Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).
ATC code
beta13
A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA).
Unique Ingredient Identifier
UNII
beta13
1.5
Basic information concerning geographical location or time.
Geotemporal metadata
true
beta13
Metadata concerning the software, hardware or other aspects of a computer system.
System metadata
beta13
1.15
A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.
Sequence feature name
true
beta13
Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.
Experimental measurement data
Experimentally measured data
Measured data
Measurement
Measurement data
Measurement metadata
Raw experimental data
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
Experimental measurement
beta13
Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.
Such data as found in Affymetrix CEL or GPR files.
Raw microarray data
beta13
Data generated from processing and analysis of probe set data from a microarray experiment.
Gene annotation (expression)
Gene expression report
Microarray probe set data
Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.
Processed microarray data
beta13
The final processed (normalised) data for a set of hybridisations in a microarray experiment.
Gene expression data matrix
Normalised microarray data
This combines data from all hybridisations.
Gene expression matrix
beta13
Annotation on a biological sample, for example experimental factors and their values.
This might include compound and dose in a dose response experiment.
Sample annotation
beta13
Annotation on the array itself used in a microarray experiment.
This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.
Microarray metadata
beta13
1.8
Annotation on laboratory and/or data processing protocols used in an microarray experiment.
This might describe e.g. the normalisation methods used to process the raw data.
Microarray protocol annotation
true
beta13
Data concerning the hybridisations measured during a microarray experiment.
Microarray hybridisation data
beta13
1.5
A report of regions in a molecular sequence that are biased to certain characters.
Sequence features (compositionally-biased regions)
true
beta13
1.5
A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.
Nucleic acid features (difference and change)
true
beta13
The report may be based on analysis of nucleic acid sequence or structural data, or any annotation or information about specific nucleic acid 3D structure(s) or such structures in general.
A human-readable collection of information about regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.
Nucleic acid features (structure)
Quadruplexes (report)
Stem loop (report)
d-loop (report)
Nucleic acid structure report
beta13
1.8
short repetitive subsequences (repeat sequences) in a protein sequence.
Protein features report (repeats)
true
beta13
1.8
Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences.
Sequence motif matches (protein)
true
beta13
1.8
Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences.
Sequence motif matches (nucleic acid)
true
beta13
1.5
A report on displacement loops in a mitochondrial DNA sequence.
A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.
Nucleic acid features (d-loop)
true
beta13
1.5
A report on stem loops in a DNA sequence.
A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.
Nucleic acid features (stem loop)
true
beta13
An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST.
Clone or EST (report)
Gene transcript annotation
Nucleic acid features (mRNA features)
Transcript (report)
mRNA (report)
mRNA features
This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
Gene transcript report
beta13
1.8
features of non-coding or functional RNA molecules, including tRNA and rRNA.
Non-coding RNA
true
beta13
1.5
Features concerning transcription of DNA into RNA including the regulation of transcription.
This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
Transcriptional features (report)
true
beta13
1.5
A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.
Nucleic acid features (immunoglobulin gene structure)
true
beta13
1.5
Information on a 'class' node from the SCOP database.
SCOP class
true
beta13
1.5
Information on a 'fold' node from the SCOP database.
SCOP fold
true
beta13
1.5
Information on a 'superfamily' node from the SCOP database.
SCOP superfamily
true
beta13
1.5
Information on a 'family' node from the SCOP database.
SCOP family
true
beta13
1.5
Information on a 'protein' node from the SCOP database.
SCOP protein
true
beta13
1.5
Information on a 'species' node from the SCOP database.
SCOP species
true
beta13
1.8
mass spectrometry experiments.
Mass spectrometry experiment
true
beta13
Nucleic acid classification
A human-readable collection of information about a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure.
Gene annotation (homology information)
Gene annotation (homology)
Gene family annotation
Gene homology (report)
Homology information
This includes reports on on gene homologues between species.
Gene family report
beta13
An image of a protein.
Protein image
beta13
1.24
An alignment of protein sequences and/or structures.
Protein alignment
true
1.0
1.8
sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.
NGS experiment
true
1.1
An informative report about a DNA sequence assembly.
Assembly report
This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.
Sequence assembly report
1.1
An index of a genome sequence.
Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
Genome index
1.1
1.8
Report concerning genome-wide association study experiments.
GWAS report
true
1.2
The position of a cytogenetic band in a genome.
Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.
Cytoband position
1.2
CL_[0-9]{7}
Cell type ontology concept ID.
CL ID
Cell type ontology ID
1.2
Mathematical model of a network, that contains biochemical kinetics.
Kinetic model
1.3
Identifier of a COSMIC database entry.
COSMIC identifier
COSMIC ID
1.3
Identifier of a HGMD database entry.
HGMD identifier
HGMD ID
1.3
true
Unique identifier of sequence assembly.
Sequence assembly version
Sequence assembly ID
1.3
1.5
A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory.
Sequence feature type
true
1.3
1.5
An informative report on gene homologues between species.
Gene homology (report)
true
1.3
ENSGT00390000003602
Unique identifier for a gene tree from the Ensembl database.
Ensembl ID (gene tree)
Ensembl gene tree ID
1.3
A phylogenetic tree that is an estimate of the character's phylogeny.
Gene tree
1.3
A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.
Species tree
1.3
true
Name or other identifier of an entry from a biosample database.
Sample accession
Sample ID
1.3
Identifier of an object from the MGI database.
MGI accession
1.3
Name of a phenotype.
Phenotype
Phenotypes
Phenotype name
1.4
A HMM transition matrix contains the probabilities of switching from one HMM state to another.
HMM transition matrix
Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa.
Transition matrix
1.4
A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM.
HMM emission matrix
Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state.
Emission matrix
1.4
1.15
A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.
Hidden Markov model
true
1.4
true
An identifier of a data format.
Format identifier
1.5
Raw biological or biomedical image generated by some experimental technique.
Raw image
http://semanticscience.org/resource/SIO_000081
1.5
Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates.
Carbohydrate data
Carbohydrate property
1.5
1.8
Report concerning proteomics experiments.
Proteomics experiment report
true
1.5
1.8
RNAi experiments.
RNAi report
true
1.5
1.8
biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.
Simulation experiment report
true
1.7
An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.
MRT image
Magnetic resonance imaging image
Magnetic resonance tomography image
NMRI image
Nuclear magnetic resonance imaging image
MRI image
1.7
An image from a cell migration track assay.
Cell migration track image
1.7
Rate of association of a protein with another protein or some other molecule.
kon
Rate of association
1.7
Multiple gene identifiers in a specific order.
Such data are often used for genome rearrangement tools and phylogenetic tree labeling.
Gene order
1.7
The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.
Spectra
Spectrum
1.7
Spectral information for a molecule from a nuclear magnetic resonance experiment.
NMR spectra
NMR spectrum
1.8
1.21
A sketch of a small molecule made with some specialised drawing package.
Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software.
Chemical structure sketch
true
1.8
An informative report about a specific or conserved nucleic acid sequence pattern.
Nucleic acid signature
1.8
A DNA sequence.
DNA sequences
DNA sequence
1.8
An RNA sequence.
RNA sequences
RNA sequence
1.8
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
1.23
A raw RNA sequence.
RNA raw sequence
Raw RNA sequence
Raw sequence (RNA)
RNA sequence (raw)
true
1.8
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
1.23
A raw DNA sequence.
DNA raw sequence
Raw DNA sequence
Raw sequence (DNA)
DNA sequence (raw)
true
1.8
Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.
Gene sequence variations
Variations are stored along with a reference genome.
Sequence variations
1.8
A list of publications such as scientic papers or books.
Bibliography
1.8
A mapping of supplied textual terms or phrases to ontology concepts (URIs).
Ontology mapping
1.9
Any data concerning a specific biological or biomedical image.
Image-associated data
Image-related data
This can include basic provenance and technical information about the image, scientific annotation and so on.
Image metadata
1.9
A human-readable collection of information concerning a clinical trial.
Clinical trial information
Clinical trial report
1.10
A report about a biosample.
Biosample report
Reference sample report
1.10
Accession number of an entry from the Gene Expression Atlas.
Gene Expression Atlas Experiment ID
1.12
true
Identifier of an entry from a database of disease.
Disease identifier
1.12
The name of some disease.
Disease name
1.12
Some material that is used for educational (training) purposes.
OER
Open educational resource
Training material
1.12
A training course available for use on the Web.
On-line course
MOOC
Massive open online course
Online course
1.12
Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query.
Free text
Plain text
Textual search query
Text
1.14
Machine-readable biodiversity data.
Biodiversity information
OTU table
Biodiversity data
1.14
A human-readable collection of information concerning biosafety data.
Biosafety information
Biosafety report
1.14
A report about any kind of isolation of biological material.
Geographic location
Isolation source
Isolation report
1.14
Information about the ability of an organism to cause disease in a corresponding host.
Pathogenicity
Pathogenicity report
1.14
Information about the biosafety classification of an organism according to corresponding law.
Biosafety level
Biosafety classification
1.14
A report about localisation of the isolaton of biological material e.g. country or coordinates.
Geographic location
1.14
A report about any kind of isolation source of biological material e.g. blood, water, soil.
Isolation source
1.14
Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum.
Physiology parameter
1.14
Experimentally determined parameter of the morphology of an organism, e.g. size & shape.
Morphology parameter
1.14
Experimental determined parameter for the cultivation of an organism.
Cultivation conditions
Carbon source
Culture media composition
Nitrogen source
Salinity
Temperature
pH value
Cultivation parameter
1.15
Data concerning a sequencing experiment, that may be specified as an input to some tool.
Sequencing metadata name
1.15
An identifier of a flow cell of a sequencing machine.
A flow cell is used to immobilise, amplify and sequence millions of molecules at once. In Illumina machines, a flowcell is composed of 8 "lanes" which allows 8 experiments in a single analysis.
Flow cell identifier
1.15
An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced.
Lane identifier
1.15
A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13.
Run number
1.15
Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment.
This is a broad data type and is used a placeholder for other, more specific types.
Ecological data
1.15
The mean species diversity in sites or habitats at a local scale.
α-diversity
Alpha diversity data
1.15
The ratio between regional and local species diversity.
True beta diversity
β-diversity
Beta diversity data
1.15
The total species diversity in a landscape.
ɣ-diversity
Gamma diversity data
1.15
A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart.
Ordination plot
1.16
A ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data.
Enrichment report
Over-representation report
Functional enrichment report
Over-representation data
1.16
GO-term report
A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins.
GO-term enrichment report
Gene ontology concept over-representation report
Gene ontology enrichment report
Gene ontology term enrichment report
GO-term enrichment data
1.16
Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry.
False localisation rate
PTM localisation
PTM score
Localisation score
1.16
Identifier of a protein modification catalogued in the Unimod database.
Unimod ID
1.16
Identifier for mass spectrometry proteomics data in the proteomexchange.org repository.
ProteomeXchange ID
1.16
Groupings of expression profiles according to a clustering algorithm.
Clustered gene expression profiles
Clustered expression profiles
1.16
An identifier of a concept from the BRENDA ontology.
BRENDA ontology concept ID
1.16
A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations.
Annotated text
1.16
A structured query, in form of a script, that defines a database search task.
Query script
1.19
Structural 3D model (volume map) from electron microscopy.
3D EM Map
1.19
Annotation on a structural 3D EM Map from electron microscopy. This might include one or several locations in the map of the known features of a particular macromolecule.
3D EM Mask
1.19
Raw DDD movie acquisition from electron microscopy.
EM Movie
1.19
Raw acquistion from electron microscopy or average of an aligned DDD movie.
EM Micrograph
1.21
Data coming from molecular simulations, computer "experiments" on model molecules.
Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).
Molecular simulation data
1.21
Identifier of an entry from the RNA central database of annotated human miRNAs.
There are canonical and taxon-specific forms of RNAcentral ID. Canonical form e.g. urs_9or10digits identifies an RNA sequence (within the RNA central database) which may appear in multiple sequences. Taxon-specific form identifies a sequence in the specific taxon (e.g. urs_9or10digits_taxonID).
RNA central ID
1.21
A human-readable systematic collection of patient (or population) health information in a digital format.
EHR
EMR
Electronic medical record
Electronic health record
1.22
Data coming from molecular simulations, computer "experiments" on model molecules. Tipically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).
Simulation
1.22
Dynamic information of a structure molecular system coming from a molecular simulation: XYZ 3D coordinates (sometimes with their associated velocities) for every atom along time.
Trajectory data
1.22
Force field parameters: charges, masses, radii, bond lengths, bond dihedrals, etc. define the structural molecular system, and are essential for the proper description and simulation of a molecular system.
Forcefield parameters
1.22
Static information of a structure molecular system that is needed for a molecular simulation: the list of atoms, their non-bonded parameters for Van der Waals and electrostatic interactions, and the complete connectivity in terms of bonds, angles and dihedrals.
Topology data
1.22
Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots.
Density plot
Histogram
1.23
A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis.
QC metrics
QC report
Quality control metrics
Quality control report
1.23
A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak).
Read count matrix
Count matrix
1.24
Alignment (superimposition) of DNA tertiary (3D) structures.
Structure alignment (DNA)
DNA structure alignment
1.24
A score derived from the P-value to ensure correction for multiple tests. The Q-value provides an estimate of the positive False Discovery Rate (pFDR), i.e. the rate of false positives among all the cases reported positive: pFDR = FP / (FP + TP).
Adjusted P-value
FDR
Padj
pFDR
Q-values are widely used in high-throughput data analysis (e.g. detection of differentially expressed genes from transcriptome data).
Q-value
1.24
A profile HMM is a variant of a Hidden Markov model that is derived specifically from a set of (aligned) biological sequences. Profile HMMs provide the basis for a position-specific scoring system, which can be used to align sequences and search databases for related sequences.
Profile HMM
1.24
WP[0-9]+
Identifier of a pathway from the WikiPathways pathway database.
WikiPathways ID
WikiPathways pathway ID
Pathway ID (WikiPathways)
1.24
A ranked list of pathways, each associated with z-score, p-value or similar, concerning or derived from the analysis of e.g. a set of genes or proteins.
Pathway analysis results
Pathway enrichment report
Pathway over-representation report
Pathway report
Pathway term enrichment report
Pathway overrepresentation data
beta12orEarlier
Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.
SMILES
beta12orEarlier
Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.
InChI
beta12orEarlier
Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.
The general MF query format consists of a series of valid atomic symbols, with an optional number or range.
mf
beta12orEarlier
The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.
An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification.
InChIKey
beta12orEarlier
SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.
smarts
beta12orEarlier
Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.
unambiguous pure
beta12orEarlier
Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.
Non-sequence characters may be used for example for gaps.
nucleotide
http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence
beta12orEarlier
Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.
Non-sequence characters may be used for gaps and translation stop.
protein
http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence
beta12orEarlier
Alphabet for the consensus of two or more molecular sequences.
consensus
beta12orEarlier
Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.
pure nucleotide
beta12orEarlier
Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .
unambiguous pure nucleotide
beta12orEarlier
Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.
dna
http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence
beta12orEarlier
Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.
rna
http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence
beta12orEarlier
Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.
unambiguous pure dna
beta12orEarlier
Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.
pure dna
beta12orEarlier
Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.
unambiguous pure rna sequence
beta12orEarlier
Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.
pure rna
beta12orEarlier
Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.
unambiguous pure protein
beta12orEarlier
Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.
pure protein
beta12orEarlier
beta12orEarlier
Format of an entry from UniGene.
A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
UniGene entry format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the COG database of clusters of (related) protein sequences.
COG sequence cluster format
true
beta12orEarlier
Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.
Feature location
EMBL feature location
beta12orEarlier
Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).
quicktandem
beta12orEarlier
Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).
Sanger inverted repeats
beta12orEarlier
Report format for tandem repeats in a sequence (an EMBOSS report format).
EMBOSS repeat
beta12orEarlier
Format of a report on exon-intron structure generated by EMBOSS est2genome.
est2genome format
beta12orEarlier
Report format for restriction enzyme recognition sites used by EMBOSS restrict program.
restrict format
beta12orEarlier
Report format for restriction enzyme recognition sites used by EMBOSS restover program.
restover format
beta12orEarlier
Report format for restriction enzyme recognition sites used by REBASE database.
REBASE restriction sites
beta12orEarlier
Format of results of a sequence database search using FASTA.
This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)
FASTA search results format
beta12orEarlier
Format of results of a sequence database search using some variant of BLAST.
This includes score data, alignment data and summary table.
BLAST results
beta12orEarlier
Format of results of a sequence database search using some variant of MSPCrunch.
mspcrunch
beta12orEarlier
Format of results of a sequence database search using some variant of Smith Waterman.
Smith-Waterman format
beta12orEarlier
Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.
The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.
dhf
beta12orEarlier
Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.
The hits are putative ligand-binding sequences and are found from a search of a sequence database.
lhf
beta12orEarlier
Results format for searches of the InterPro database.
InterPro hits format
beta12orEarlier
Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.
The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.
InterPro protein view report format
beta12orEarlier
Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.
The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.
InterPro match table format
beta12orEarlier
Dirichlet distribution HMMER format.
HMMER Dirichlet prior
beta12orEarlier
Dirichlet distribution MEME format.
MEME Dirichlet prior
beta12orEarlier
Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.
HMMER emission and transition
beta12orEarlier
Format of a regular expression pattern from the Prosite database.
prosite-pattern
beta12orEarlier
Format of an EMBOSS sequence pattern.
EMBOSS sequence pattern
beta12orEarlier
A motif in the format generated by the MEME program.
meme-motif
beta12orEarlier
Sequence profile (sequence classifier) format used in the PROSITE database.
prosite-profile
beta12orEarlier
A profile (sequence classifier) in the format used in the JASPAR database.
JASPAR format
beta12orEarlier
Format of the model of random sequences used by MEME.
MEME background Markov model
beta12orEarlier
Format of a hidden Markov model representation used by the HMMER package.
HMMER format
beta12orEarlier
FASTA-style format for multiple sequences aligned by HMMER package to an HMM.
HMMER-aln
beta12orEarlier
Format of multiple sequences aligned by DIALIGN package.
DIALIGN format
beta12orEarlier
EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.
The format is clustal-like and includes annotation of domain family classification information.
daf
beta12orEarlier
Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.
Sequence-MEME profile alignment
beta12orEarlier
Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.
HMMER profile alignment (sequences versus HMMs)
beta12orEarlier
Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.
HMMER profile alignment (HMM versus sequences)
beta12orEarlier
Format of PHYLIP phylogenetic distance matrix data.
Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).
Phylip distance matrix
beta12orEarlier
Dendrogram (tree file) format generated by ClustalW.
ClustalW dendrogram
beta12orEarlier
Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.
Phylip tree raw
beta12orEarlier
PHYLIP file format for continuous quantitative character data.
Phylip continuous quantitative characters
beta12orEarlier
beta12orEarlier
Format of phylogenetic property data.
Phylogenetic property values format
true
beta12orEarlier
PHYLIP file format for phylogenetics character frequency data.
Phylip character frequencies format
beta12orEarlier
Format of PHYLIP discrete states data.
Phylip discrete states format
beta12orEarlier
Format of PHYLIP cliques data.
Phylip cliques format
beta12orEarlier
Phylogenetic tree data format used by the PHYLIP program.
Phylip tree format
beta12orEarlier
The format of an entry from the TreeBASE database of phylogenetic data.
TreeBASE format
beta12orEarlier
The format of an entry from the TreeFam database of phylogenetic data.
TreeFam format
beta12orEarlier
Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.
Phylip tree distance format
beta12orEarlier
Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).
The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.
dssp
beta12orEarlier
Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).
hssp
beta12orEarlier
Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.
Vienna RNA format
Vienna RNA secondary structure format
Dot-bracket format
beta12orEarlier
Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.
Vienna local RNA secondary structure format
beta12orEarlier
Format of an entry (or part of an entry) from the PDB database.
PDB entry format
PDB database entry format
beta12orEarlier
Entry format of PDB database in PDB format.
PDB format
PDB
beta12orEarlier
Entry format of PDB database in mmCIF format.
mmCIF
beta12orEarlier
Entry format of PDB database in PDBML (XML) format.
PDBML
beta12orEarlier
beta12orEarlier
Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.
Domainatrix 3D-1D scoring matrix format
true
beta12orEarlier
Amino acid index format used by the AAindex database.
aaindex
beta12orEarlier
beta12orEarlier
Format of an entry from IntEnz (The Integrated Relational Enzyme Database).
IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
IntEnz enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the BRENDA enzyme database.
BRENDA enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the KEGG REACTION database of biochemical reactions.
KEGG REACTION enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the KEGG ENZYME database.
KEGG ENZYME enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the proto section of the REBASE enzyme database.
REBASE proto enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the withrefm section of the REBASE enzyme database.
REBASE withrefm enzyme report format
true
beta12orEarlier
Format of output of the Pcons Model Quality Assessment Program (MQAP).
Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.
Pcons report format
beta12orEarlier
Format of output of the ProQ protein model quality predictor.
ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.
ProQ report format
beta12orEarlier
beta12orEarlier
Format of SMART domain assignment data.
The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.
SMART domain assignment report format
true
beta12orEarlier
beta12orEarlier
Entry format for the BIND database of protein interaction.
BIND entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the IntAct database of protein interaction.
IntAct entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.
This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
InterPro entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.
References are included and a functional inference is made where possible.
InterPro entry abstract format
true
beta12orEarlier
beta12orEarlier
Entry format for the Gene3D protein secondary database.
Gene3D entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the PIRSF protein secondary database.
PIRSF entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the PRINTS protein secondary database.
PRINTS entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the Panther library of protein families and subfamilies.
Panther Families and HMMs entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the Pfam protein secondary database.
Pfam entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the SMART protein secondary database.
SMART entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the Superfamily protein secondary database.
Superfamily entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the TIGRFam protein secondary database.
TIGRFam entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the ProDom protein domain classification database.
ProDom entry format
true
beta12orEarlier
beta12orEarlier
Entry format for the FSSP database.
FSSP entry format
true
beta12orEarlier
A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).
findkm
beta12orEarlier
beta12orEarlier
Entry format of Ensembl genome database.
Ensembl gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of DictyBase genome database.
DictyBase gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of Candida Genome database.
CGD gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of DragonDB genome database.
DragonDB gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of EcoCyc genome database.
EcoCyc gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of FlyBase genome database.
FlyBase gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of Gramene genome database.
Gramene gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of KEGG GENES genome database.
KEGG GENES gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the Maize genetics and genomics database (MaizeGDB).
MaizeGDB gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the Mouse Genome Database (MGD).
MGD gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the Rat Genome Database (RGD).
RGD gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the Saccharomyces Genome Database (SGD).
SGD gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the Sanger GeneDB genome database.
GeneDB gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of The Arabidopsis Information Resource (TAIR) genome database.
TAIR gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the WormBase genomes database.
WormBase gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the Zebrafish Information Network (ZFIN) genome database.
ZFIN gene report format
true
beta12orEarlier
beta12orEarlier
Entry format of the TIGR genome database.
TIGR gene report format
true
beta12orEarlier
beta12orEarlier
Entry format for the dbSNP database.
dbSNP polymorphism report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the OMIM database of genotypes and phenotypes.
OMIM entry format
true
beta12orEarlier
beta12orEarlier
Format of a record from the HGVbase database of genotypes and phenotypes.
HGVbase entry format
true
beta12orEarlier
beta12orEarlier
Format of a record from the HIVDB database of genotypes and phenotypes.
HIVDB entry format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the KEGG DISEASE database.
KEGG DISEASE entry format
true
beta12orEarlier
Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program.
Primer3 primer
beta12orEarlier
A format of raw sequence read data from an Applied Biosystems sequencing machine.
ABI
beta12orEarlier
Format of MIRA sequence trace information file.
mira
beta12orEarlier
Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.
CAF
beta12orEarlier
Sequence assembly project file EXP format.
Affymetrix EXP format
EXP
EXP
beta12orEarlier
Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.
SCF
beta12orEarlier
PHD sequence trace format to store serialised chromatogram data (reads).
PHD
beta12orEarlier
Format of Affymetrix data file of raw image data.
Affymetrix image data file format
dat
beta12orEarlier
Format of Affymetrix data file of information about (raw) expression levels of the individual probes.
Affymetrix probe raw data format
cel
beta12orEarlier
Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.
affymetrix
beta12orEarlier
beta12orEarlier
Entry format for the ArrayExpress microarrays database.
ArrayExpress entry format
true
beta12orEarlier
Affymetrix data file format for information about experimental conditions and protocols.
Affymetrix experimental conditions data file format
affymetrix-exp
beta12orEarlier
Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.
Affymetrix probe normalised data format
CHP
beta12orEarlier
beta12orEarlier
Format of an entry from the Electron Microscopy DataBase (EMDB).
EMDB entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.
KEGG PATHWAY entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the MetaCyc metabolic pathways database.
MetaCyc entry format
true
beta12orEarlier
beta12orEarlier
The format of a report from the HumanCyc metabolic pathways database.
HumanCyc entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the INOH signal transduction pathways database.
INOH entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the PATIKA biological pathways database.
PATIKA entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the reactome biological pathways database.
Reactome entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the aMAZE biological pathways and molecular interactions database.
aMAZE entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the CPDB database.
CPDB entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the Panther Pathways database.
Panther Pathways entry format
true
beta12orEarlier
Format of Taverna workflows.
Taverna workflow format
beta12orEarlier
beta12orEarlier
Format of mathematical models from the BioModel database.
Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
BioModel mathematical model format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the KEGG LIGAND chemical database.
KEGG LIGAND entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the KEGG COMPOUND database.
KEGG COMPOUND entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the KEGG PLANT database.
KEGG PLANT entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the KEGG GLYCAN database.
KEGG GLYCAN entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from PubChem.
PubChem entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from a database of chemical structures and property predictions.
ChemSpider entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from Chemical Entities of Biological Interest (ChEBI).
ChEBI includes an ontological classification defining relations between entities or classes of entities.
ChEBI entry format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the MSDchem ligand dictionary.
MSDchem ligand dictionary entry format
true
beta12orEarlier
The format of an entry from the HET group dictionary (HET groups from PDB files).
HET group dictionary entry format
beta12orEarlier
beta12orEarlier
The format of an entry from the KEGG DRUG database.
KEGG DRUG entry format
true
beta12orEarlier
Format of bibliographic reference as used by the PubMed database.
PubMed citation
beta12orEarlier
Format for abstracts of scientific articles from the Medline database.
Bibliographic reference information including citation information is included
Medline Display Format
beta12orEarlier
CiteXplore 'core' citation format including title, journal, authors and abstract.
CiteXplore-core
beta12orEarlier
CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references.
CiteXplore-all
beta12orEarlier
Article format of the PubMed Central database.
pmc
beta12orEarlier
The format of iHOP (Information Hyperlinked over Proteins) text-mining result.
iHOP format
beta12orEarlier
OSCAR format of annotated chemical text.
OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts, and chemical data from a document.
OSCAR format
beta12orEarlier
beta13
Format of an ATOM record (describing data for an individual atom) from a PDB file.
PDB atom record format
true
beta12orEarlier
beta12orEarlier
Format of CATH domain classification information for a polypeptide chain.
The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.
CATH chain report format
true
beta12orEarlier
beta12orEarlier
Format of CATH domain classification information for a protein PDB file.
The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.
CATH PDB report format
true
beta12orEarlier
beta12orEarlier
Entry (gene) format of the NCBI database.
NCBI gene report format
true
beta12orEarlier
beta12orEarlier
Moby:GI_Gene
Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.
This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.
GeneIlluminator gene report format
true
beta12orEarlier
beta12orEarlier
Moby:BacMapGeneCard
Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database.
BacMap gene card format
true
beta12orEarlier
beta12orEarlier
Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).
ColiCard report format
true
beta12orEarlier
Map of a plasmid (circular DNA) in PlasMapper TextMap format.
PlasMapper TextMap
beta12orEarlier
Phylogenetic tree Newick (text) format.
nh
newick
beta12orEarlier
Phylogenetic tree TreeCon (text) format.
TreeCon format
beta12orEarlier
Phylogenetic tree Nexus (text) format.
Nexus format
beta12orEarlier
true
Data model
A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
Data format
Exchange format
File format
The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
Format
"http://purl.obolibrary.org/obo/IAO_0000098"
"http://purl.org/dc/elements/1.1/format"
http://en.wikipedia.org/wiki/File_format
http://en.wikipedia.org/wiki/List_of_file_formats
http://purl.org/biotop/biotop.owl#MachineLanguage
http://purl.org/biotop/biotop.owl#Quality
http://semanticscience.org/resource/SIO_000612
http://semanticscience.org/resource/SIO_000618
http://wsio.org/compression_004
http://www.ifomis.org/bfo/1.1/snap#Continuant
http://www.ifomis.org/bfo/1.1/snap#Quality
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality
http://www.onto-med.de/ontologies/gfo.owl#Perpetuant
http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure
Data model
A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.)
File format
File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages.
beta12orEarlier
beta13
Data format for an individual atom.
Atomic data format
true
beta12orEarlier
true
Data format for a molecular sequence record.
Sequence record format
beta12orEarlier
true
Data format for molecular sequence feature information.
Sequence feature annotation format
beta12orEarlier
true
Data format for molecular sequence alignment information.
Alignment format
beta12orEarlier
ACEDB sequence format.
acedb
beta12orEarlier
beta12orEarlier
Clustalw output format.
clustal sequence format
true
beta12orEarlier
Codata entry format.
codata
beta12orEarlier
Fasta format variant with database name before ID.
dbid
beta12orEarlier
EMBL entry format.
EMBL
EMBL sequence format
EMBL format
beta12orEarlier
Staden experiment file format.
Staden experiment format
beta12orEarlier
FASTA format including NCBI-style IDs.
FASTA format
FASTA sequence format
FASTA
beta12orEarlier
fastq
fq
FASTQ short read format ignoring quality scores.
FASTAQ
fq
FASTQ
beta12orEarlier
FASTQ Illumina 1.3 short read format.
FASTQ-illumina
beta12orEarlier
FASTQ short read format with phred quality.
FASTQ-sanger
beta12orEarlier
FASTQ Solexa/Illumina 1.0 short read format.
FASTQ-solexa
beta12orEarlier
Fitch program format.
fitch program
beta12orEarlier
GCG sequence file format.
GCG SSF
GCG SSF (single sequence file) file format.
GCG
beta12orEarlier
Genbank entry format.
GenBank
GenBank format
beta12orEarlier
Genpept protein entry format.
Currently identical to refseqp format
genpept
beta12orEarlier
GFF feature file format with sequence in the header.
GFF2-seq
beta12orEarlier
GFF3 feature file format with sequence.
GFF3-seq
beta12orEarlier
FASTA sequence format including NCBI-style GIs.
giFASTA format
beta12orEarlier
Hennig86 output sequence format.
hennig86
beta12orEarlier
Intelligenetics sequence format.
ig
beta12orEarlier
Intelligenetics sequence format (strict version).
igstrict
beta12orEarlier
Jackknifer interleaved and non-interleaved sequence format.
jackknifer
beta12orEarlier
Mase program sequence format.
mase format
beta12orEarlier
Mega interleaved and non-interleaved sequence format.
mega-seq
beta12orEarlier
GCG MSF (multiple sequence file) file format.
GCG MSF
beta12orEarlier
NBRF/PIR entry sequence format.
nbrf
pir
nbrf/pir
beta12orEarlier
Nexus/paup interleaved sequence format.
nexus-seq
beta12orEarlier
PDB sequence format (ATOM lines).
pdb format in EMBOSS.
pdbatom
beta12orEarlier
PDB nucleotide sequence format (ATOM lines).
pdbnuc format in EMBOSS.
pdbatomnuc
beta12orEarlier
PDB nucleotide sequence format (SEQRES lines).
pdbnucseq format in EMBOSS.
pdbseqresnuc
beta12orEarlier
PDB sequence format (SEQRES lines).
pdbseq format in EMBOSS.
pdbseqres
beta12orEarlier
Plain old FASTA sequence format (unspecified format for IDs).
Pearson format
beta12orEarlier
beta12orEarlier
Phylip interleaved sequence format.
phylip sequence format
true
beta12orEarlier
beta12orEarlier
PHYLIP non-interleaved sequence format.
phylipnon sequence format
true
beta12orEarlier
Raw sequence format with no non-sequence characters.
raw
beta12orEarlier
Refseq protein entry sequence format.
Currently identical to genpept format
refseqp
beta12orEarlier
beta12orEarlier
Selex sequence format.
selex sequence format
true
beta12orEarlier
Staden suite sequence format.
Staden format
beta12orEarlier
Stockholm multiple sequence alignment format (used by Pfam and Rfam).
Stockholm format
beta12orEarlier
DNA strider output sequence format.
strider format
beta12orEarlier
UniProtKB entry sequence format.
SwissProt format
UniProt format
UniProtKB format
beta12orEarlier
Plain text sequence format (essentially unformatted).
plain text format (unformatted)
beta12orEarlier
beta12orEarlier
Treecon output sequence format.
treecon sequence format
true
beta12orEarlier
NCBI ASN.1-based sequence format.
ASN.1 sequence format
beta12orEarlier
DAS sequence (XML) format (any type).
das sequence format
DAS format
beta12orEarlier
DAS sequence (XML) format (nucleotide-only).
The use of this format is deprecated.
dasdna
beta12orEarlier
EMBOSS debugging trace sequence format of full internal data content.
debug-seq
beta12orEarlier
Jackknifer output sequence non-interleaved format.
jackknifernon
beta12orEarlier
beta12orEarlier
Mega non-interleaved output sequence format.
meganon sequence format
true
beta12orEarlier
NCBI FASTA sequence format with NCBI-style IDs.
There are several variants of this.
NCBI format
beta12orEarlier
Nexus/paup non-interleaved sequence format.
nexusnon
beta12orEarlier
General Feature Format (GFF) of sequence features.
GFF2
beta12orEarlier
Generic Feature Format version 3 (GFF3) of sequence features.
GFF3
beta12orEarlier
1.7
PIR feature format.
pir
true
beta12orEarlier
beta12orEarlier
Swiss-Prot feature format.
swiss feature
true
beta12orEarlier
DAS GFF (XML) feature format.
DASGFF feature
das feature
DASGFF
beta12orEarlier
EMBOSS debugging trace feature format of full internal data content.
debug-feat
beta12orEarlier
beta12orEarlier
EMBL feature format.
EMBL feature
true
beta12orEarlier
beta12orEarlier
Genbank feature format.
GenBank feature
true
beta12orEarlier
ClustalW format for (aligned) sequences.
clustal
ClustalW format
beta12orEarlier
EMBOSS alignment format for debugging trace of full internal data content.
debug
beta12orEarlier
Fasta format for (aligned) sequences.
FASTA-aln
beta12orEarlier
Pearson MARKX0 alignment format.
markx0
beta12orEarlier
Pearson MARKX1 alignment format.
markx1
beta12orEarlier
Pearson MARKX10 alignment format.
markx10
beta12orEarlier
Pearson MARKX2 alignment format.
markx2
beta12orEarlier
Pearson MARKX3 alignment format.
markx3
beta12orEarlier
Alignment format for start and end of matches between sequence pairs.
match
beta12orEarlier
Mega format for (typically aligned) sequences.
mega
beta12orEarlier
Mega non-interleaved format for (typically aligned) sequences.
meganon
beta12orEarlier
beta12orEarlier
MSF format for (aligned) sequences.
msf alignment format
true
beta12orEarlier
beta12orEarlier
Nexus/paup format for (aligned) sequences.
nexus alignment format
true
beta12orEarlier
beta12orEarlier
Nexus/paup non-interleaved format for (aligned) sequences.
nexusnon alignment format
true
beta12orEarlier
EMBOSS simple sequence pair alignment format.
pair
beta12orEarlier
http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format
Phylip format for (aligned) sequences.
PHYLIP
PHYLIP interleaved format
ph
phy
PHYLIP format
beta12orEarlier
http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format
Phylip non-interleaved format for (aligned) sequences.
PHYLIP sequential format
phylipnon
PHYLIP sequential
beta12orEarlier
Alignment format for score values for pairs of sequences.
scores format
beta12orEarlier
SELEX format for (aligned) sequences.
selex
beta12orEarlier
EMBOSS simple multiple alignment format.
EMBOSS simple format
beta12orEarlier
Simple multiple sequence (alignment) format for SRS.
srs format
beta12orEarlier
Simple sequence pair (alignment) format for SRS.
srspair
beta12orEarlier
T-Coffee program alignment format.
T-Coffee format
beta12orEarlier
Treecon format for (aligned) sequences.
TreeCon-seq
beta12orEarlier
true
Data format for a phylogenetic tree.
Phylogenetic tree format
beta12orEarlier
true
Data format for a biological pathway or network.
Biological pathway or network format
beta12orEarlier
true
Data format for a sequence-profile alignment.
Sequence-profile alignment format
beta12orEarlier
beta12orEarlier
Data format for a sequence-HMM profile alignment.
Sequence-profile alignment (HMM) format
true
beta12orEarlier
Data format for an amino acid index.
Amino acid index format
beta12orEarlier
true
Data format for a full-text scientific article.
Literature format
Article format
beta12orEarlier
true
Data format of a report from text mining.
Text mining report format
beta12orEarlier
true
Data format for reports on enzyme kinetics.
Enzyme kinetics report format
beta12orEarlier
true
Format of a report on a chemical compound.
Chemical compound annotation format
Chemical structure format
Small molecule report format
Small molecule structure format
Chemical data format
beta12orEarlier
true
Format of a report on a particular locus, gene, gene system or groups of genes.
Gene features format
Gene annotation format
beta12orEarlier
true
Programming language
Script format
Format of a workflow.
Workflow format
beta12orEarlier
true
Data format for a molecular tertiary structure.
Tertiary structure format
beta12orEarlier
1.2
Data format for a biological model.
Biological model format
true
beta12orEarlier
true
Text format of a chemical formula.
Chemical formula format
beta12orEarlier
true
Format of raw (unplotted) phylogenetic data.
Phylogenetic character data format
beta12orEarlier
Format of phylogenetic continuous quantitative character data.
Phylogenetic continuous quantitative character format
beta12orEarlier
Format of phylogenetic discrete states data.
Phylogenetic discrete states format
beta12orEarlier
Format of phylogenetic cliques data.
Phylogenetic tree report (cliques) format
beta12orEarlier
Format of phylogenetic invariants data.
Phylogenetic tree report (invariants) format
beta12orEarlier
beta12orEarlier
Annotation format for electron microscopy models.
Electron microscopy model format
true
beta12orEarlier
true
Format for phylogenetic tree distance data.
Phylogenetic tree report (tree distances) format
beta12orEarlier
1.0
Format for sequence polymorphism data.
Polymorphism report format
true
beta12orEarlier
true
Format for reports on a protein family.
Protein family report format
beta12orEarlier
true
Molecular interaction format
Format for molecular interaction data.
Protein interaction format
beta12orEarlier
true
Format for sequence assembly data.
Sequence assembly format
beta12orEarlier
Format for information about a microarray experimental per se (not the data generated from that experiment).
Microarray experiment data format
beta12orEarlier
Format for sequence trace data (i.e. including base call information).
Sequence trace format
beta12orEarlier
true
Format of a file of gene expression data, e.g. a gene expression matrix or profile.
Gene expression data format
Gene expression report format
beta12orEarlier
beta12orEarlier
Format of a report on genotype / phenotype information.
Genotype and phenotype annotation format
true
beta12orEarlier
true
Format of a map of (typically one) molecular sequence annotated with features.
Map format
beta12orEarlier
true
Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence.
Nucleic acid features (primers) format
beta12orEarlier
true
Format of a report of general information about a specific protein.
Protein report format
beta12orEarlier
beta12orEarlier
Format of a report of general information about a specific enzyme.
Protein report (enzyme) format
true
beta12orEarlier
Format of a matrix of 3D-1D scores (amino acid environment probabilities).
3D-1D scoring matrix format
beta12orEarlier
true
Format of a report on the quality of a protein three-dimensional model.
Protein structure report (quality evaluation) format
beta12orEarlier
true
Format of a report on sequence hits and associated data from searching a sequence database.
Database hits (sequence) format
beta12orEarlier
true
Format of a matrix of genetic distances between molecular sequences.
Sequence distance matrix format
beta12orEarlier
true
Format of a sequence motif.
Sequence motif format
beta12orEarlier
true
Format of a sequence profile.
Sequence profile format
beta12orEarlier
Format of a hidden Markov model.
Hidden Markov model format
beta12orEarlier
true
Data format of a dirichlet distribution.
Dirichlet distribution format
beta12orEarlier
true
Data format for the emission and transition counts of a hidden Markov model.
HMM emission and transition counts format
beta12orEarlier
true
Format for secondary structure (predicted or real) of an RNA molecule.
RNA secondary structure format
beta12orEarlier
true
Format for secondary structure (predicted or real) of a protein molecule.
Protein secondary structure format
beta12orEarlier
true
Format used to specify range(s) of sequence positions.
Sequence range format
beta12orEarlier
Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.
pure
beta12orEarlier
Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.
unpure
beta12orEarlier
Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.
unambiguous sequence
beta12orEarlier
Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.
ambiguous
beta12orEarlier
true
Format used for map of repeats in molecular (typically nucleotide) sequences.
Sequence features (repeats) format
beta12orEarlier
true
Format used for report on restriction enzyme recognition sites in nucleotide sequences.
Nucleic acid features (restriction sites) format
beta12orEarlier
1.10
Format used for report on coding regions in nucleotide sequences.
Gene features (coding region) format
true
beta12orEarlier
true
Format used for clusters of molecular sequences.
Sequence cluster format
beta12orEarlier
Format used for clusters of protein sequences.
Sequence cluster format (protein)
beta12orEarlier
Format used for clusters of nucleotide sequences.
Sequence cluster format (nucleic acid)
beta12orEarlier
beta13
Format used for clusters of genes.
Gene cluster format
true
beta12orEarlier
A text format resembling EMBL entry format.
This concept may be used for the many non-standard EMBL-like text formats.
EMBL-like (text)
beta12orEarlier
A text format resembling FASTQ short read format.
This concept may be used for non-standard FASTQ short read-like formats.
FASTQ-like format (text)
beta12orEarlier
XML format for EMBL entries.
EMBLXML
beta12orEarlier
XML format for EMBL entries.
cdsxml
beta12orEarlier
XML format for EMBL entries.
insdxml
beta12orEarlier
Geneseq sequence format.
geneseq
beta12orEarlier
A text sequence format resembling uniprotkb entry format.
UniProt-like (text)
beta12orEarlier
1.8
UniProt entry sequence format.
UniProt format
true
beta12orEarlier
1.8
ipi sequence format.
ipi
true
beta12orEarlier
Abstract format used by MedLine database.
medline
beta12orEarlier
true
Format used for ontologies.
Ontology format
beta12orEarlier
A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.
OBO format
beta12orEarlier
A serialisation format conforming to the Web Ontology Language (OWL) model.
OWL format
beta12orEarlier
A text format resembling FASTA format.
This concept may also be used for the many non-standard FASTA-like formats.
FASTA-like (text)
http://filext.com/file-extension/FASTA
beta12orEarlier
1.8
Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.
Sequence record full format
true
beta12orEarlier
1.8
Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.
Sequence record lite format
true
beta12orEarlier
An XML format for EMBL entries.
This is a placeholder for other more specific concepts. It should not normally be used for annotation.
EMBL format (XML)
beta12orEarlier
A text format resembling GenBank entry (plain text) format.
This concept may be used for the non-standard GenBank-like text formats.
GenBank-like format (text)
beta12orEarlier
Text format for a sequence feature table.
Sequence feature table format (text)
beta12orEarlier
1.0
Format of a report on organism strain data / cell line.
Strain data format
true
beta12orEarlier
beta12orEarlier
Format for a report of strain data as used for CIP database entries.
CIP strain data format
true
beta12orEarlier
beta12orEarlier
PHYLIP file format for phylogenetic property data.
phylip property values
true
beta12orEarlier
beta12orEarlier
Entry format (HTML) for the STRING database of protein interaction.
STRING entry format (HTML)
true
beta12orEarlier
Entry format (XML) for the STRING database of protein interaction.
STRING entry format (XML)
beta12orEarlier
GFF feature format (of indeterminate version).
GFF
beta12orEarlier
Gene Transfer Format (GTF), a restricted version of GFF.
GTF
beta12orEarlier
FASTA format wrapped in HTML elements.
FASTA-HTML
beta12orEarlier
EMBL entry format wrapped in HTML elements.
EMBL-HTML
beta12orEarlier
beta12orEarlier
Format of an entry from the BioCyc enzyme database.
BioCyc enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of an entry from the Enzyme nomenclature database (ENZYME).
ENZYME enzyme report format
true
beta12orEarlier
beta12orEarlier
Format of a report on a gene from the PseudoCAP database.
PseudoCAP gene report format
true
beta12orEarlier
beta12orEarlier
Format of a report on a gene from the GeneCards database.
GeneCards gene report format
true
beta12orEarlier
Textual format.
Plain text format
txt
Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).
Textual format
http://filext.com/file-extension/TXT
http://www.iana.org/assignments/media-types/media-types.xhtml#text
http://www.iana.org/assignments/media-types/text/plain
beta12orEarlier
HTML format.
Hypertext Markup Language
HTML
http://filext.com/file-extension/HTML
beta12orEarlier
xml
eXtensible Markup Language (XML) format.
eXtensible Markup Language
Data in XML format can be serialised into text, or binary format.
XML
beta12orEarlier
true
Binary format.
Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.
Binary format
beta12orEarlier
beta13
Typical textual representation of a URI.
URI format
true
beta12orEarlier
beta12orEarlier
The format of an entry from the NCI-Nature pathways database.
NCI-Nature pathway entry format
true
beta12orEarlier
true
A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented.
Format (typed)
This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches.
Format (by type of data)
beta12orEarlier
Any ontology allowed, none mandatory. Preferrably with URIs but URIs are not mandatory. Non-ontology terms are also allowed as the last resort in case of a lack of suitable ontology.
'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioXSD in XML' is the XML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'.
BioXSD
BioXSD data model
BioXSD format
BioXSD/GTrack
BioXSD|BioJSON|BioYAML
BioXSD|GTrack
BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming.
BioXSD XML
BioXSD XML format
BioXSD in XML
BioXSD in XML format
BioXSD+XML
BioXSD (XML)
beta12orEarlier
A serialisation format conforming to the Resource Description Framework (RDF) model.
Resource Description Framework format
RDF
Resource Description Framework
RDF format
beta12orEarlier
Genbank entry format wrapped in HTML elements.
GenBank-HTML
beta12orEarlier
beta12orEarlier
Format of a report on protein features (domain composition).
Protein features (domains) format
true
beta12orEarlier
A format resembling EMBL entry (plain text) format.
This concept may be used for the many non-standard EMBL-like formats.
EMBL-like format
beta12orEarlier
A format resembling FASTQ short read format.
This concept may be used for non-standard FASTQ short read-like formats.
FASTQ-like format
beta12orEarlier
A format resembling FASTA format.
This concept may be used for the many non-standard FASTA-like formats.
FASTA-like
beta12orEarlier
A sequence format resembling uniprotkb entry format.
uniprotkb-like format
beta12orEarlier
Format for a sequence feature table.
Sequence feature table format
beta12orEarlier
OBO ontology text format.
OBO
beta12orEarlier
OBO ontology XML format.
OBO-XML
beta12orEarlier
Data format for a molecular sequence record.
Sequence record format (text)
beta12orEarlier
Data format for a molecular sequence record.
Sequence record format (XML)
beta12orEarlier
XML format for a sequence feature table.
Sequence feature table format (XML)
beta12orEarlier
Text format for molecular sequence alignment information.
Alignment format (text)
beta12orEarlier
XML format for molecular sequence alignment information.
Alignment format (XML)
beta12orEarlier
Text format for a phylogenetic tree.
Phylogenetic tree format (text)
beta12orEarlier
XML format for a phylogenetic tree.
Phylogenetic tree format (XML)
beta12orEarlier
An XML format resembling EMBL entry format.
This concept may be used for the any non-standard EMBL-like XML formats.
EMBL-like (XML)
beta12orEarlier
A format resembling GenBank entry (plain text) format.
This concept may be used for the non-standard GenBank-like formats.
GenBank-like format
beta12orEarlier
beta12orEarlier
Entry format for the STRING database of protein interaction.
STRING entry format
true
beta12orEarlier
Text format for sequence assembly data.
Sequence assembly format (text)
beta12orEarlier
beta13
Text format (representation) of amino acid residues.
Amino acid identifier format
true
beta12orEarlier
Alphabet for a molecular sequence without any unknown positions or ambiguity characters.
completely unambiguous
beta12orEarlier
Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.
completely unambiguous pure
beta12orEarlier
Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .
completely unambiguous pure nucleotide
beta12orEarlier
Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.
completely unambiguous pure dna
beta12orEarlier
Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.
completely unambiguous pure rna sequence
beta12orEarlier
true
Format of a raw molecular sequence (i.e. the alphabet used).
Raw sequence format
http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence
beta12orEarlier
BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.
BAM
beta12orEarlier
Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.
The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.
SAM
beta12orEarlier
Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.
SBML
beta12orEarlier
Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.
completely unambiguous pure protein
beta12orEarlier
true
Format of a bibliographic reference.
Bibliographic reference format
beta12orEarlier
Format of a sequence annotation track.
Sequence annotation track format
beta12orEarlier
Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.
Alignment format (pair only)
beta12orEarlier
true
Format of sequence variation annotation.
Sequence variation annotation format
beta12orEarlier
Some variant of Pearson MARKX alignment format.
markx0 variant
beta12orEarlier
Some variant of Mega format for (typically aligned) sequences.
mega variant
beta12orEarlier
Some variant of Phylip format for (aligned) sequences.
Phylip format variant
beta12orEarlier
AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.
AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).
AB1
beta12orEarlier
ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).
ACE
beta12orEarlier
Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.
BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).
BED
beta12orEarlier
bigBed format for large sequence annotation tracks, similar to textual BED format.
bigBed
beta12orEarlier
Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.
WIG
beta12orEarlier
bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.
bigWig
beta12orEarlier
PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.
PSL
beta12orEarlier
Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.
Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.
MAF
beta12orEarlier
2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'.
2bit
beta12orEarlier
.nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'.
.nib
beta12orEarlier
genePred table format for gene prediction tracks.
genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.
genePred
beta12orEarlier
Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.
pgSnp
beta12orEarlier
axt format of alignments, typically produced from BLASTZ.
axt
beta12orEarlier
LAV format of alignments generated by BLASTZ and LASTZ.
LAV
beta12orEarlier
Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).
Pileup
beta12orEarlier
Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
VCF
beta12orEarlier
Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.
SRF
beta12orEarlier
ZTR format for storing chromatogram data from DNA sequencing instruments.
ZTR
beta12orEarlier
Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.
GVF
beta12orEarlier
BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
BCF
beta13
true
Format of a matrix (array) of numerical values.
Matrix format
beta13
true
Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).
Protein domain classification format
beta13
Format of raw SCOP domain classification data files.
These are the parsable data files provided by SCOP.
Raw SCOP domain classification format
beta13
Format of raw CATH domain classification data files.
These are the parsable data files provided by CATH.
Raw CATH domain classification format
beta13
Format of summary of domain classification information for a CATH domain.
The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
CATH domain report format
1.0
Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.
SBRML
1.0
BioPAX is an exchange format for pathway data, with its data model defined in OWL.
BioPAX
1.0
EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.
EBI Application Result XML
1.0
XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.
MIF
PSI MI XML (MIF)
1.0
phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.
phyloXML
1.0
NeXML is a standardised XML format for rich phyloinformatic data.
NeXML
1.0
MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).
MAGE-ML
1.0
MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).
MAGE-TAB
1.0
GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).
GCDML
1.0
'GTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GTrack' is the tabular format for representing features of sequences and genomes.
GTrack ecosystem of formats
GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation ("machine understandability").
BioXSD/GTrack GTrack
BioXSD|GTrack GTrack
GTrack format
GTrack|BTrack|GSuite GTrack
GTrack|GSuite|BTrack GTrack
GTrack
1.0
true
Data format for a report of information derived from a biological pathway or network.
Biological pathway or network report format
1.0
true
Data format for annotation on a laboratory experiment.
Experiment annotation format
1.2
Cytoband format for chromosome cytobands.
Reflects a UCSC Browser DB table.
Cytoband format
1.2
CopasiML, the native format of COPASI.
CopasiML
1.2
CellML, the format for mathematical models of biological and other networks.
CellML
1.2
Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.
PSI MI TAB (MITAB)
1.2
Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.
PSI-PAR
1.2
mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.
mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.
mzML
1.2
true
Format for mass pectra and derived data, include peptide sequences etc.
Mass spectrometry data format
1.2
TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.
TraML
1.2
mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines.
mzIdentML
1.2
mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.
mzQuantML
1.2
GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.
GelML
1.2
spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics.
spML
1.2
A human-readable encoding for the Web Ontology Language (OWL).
OWL Functional Syntax
1.2
A syntax for writing OWL class expressions.
This format was influenced by the OWL Abstract Syntax and the DL style syntax.
Manchester OWL Syntax
1.2
A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort".
This format is used in Protege 4.
KRSS2 Syntax
1.2
The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs.
The SPARQL Query Language incorporates a very similar syntax.
Turtle
1.2
nt
A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.
N-Triples should not be confused with Notation 3 which is a superset of Turtle.
N-Triples
1.2
n3
A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind.
N3
Notation3
1.2
rdf
Resource Description Framework (RDF) XML format.
RDF/XML is a serialisation syntax for OWL DL, but not for OWL Full.
RDF/XML
http://www.ebi.ac.uk/SWO/data/SWO_3000006
1.2
OWL ontology XML serialisation format.
OWL
OWL/XML
1.3
The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.
A2M
1.3
Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.
Standard flowgram format
SFF
1.3
The MAP file describes SNPs and is used by the Plink package.
Plink MAP
MAP
1.3
The PED file describes individuals and genetic data and is used by the Plink package.
Plink PED
PED
1.3
true
Data format for a metadata on an individual and their genetic data.
Individual genetic data format
1.3
The PED/MAP file describes data used by the Plink package.
Plink PED/MAP
PED/MAP
1.3
File format of a CT (Connectivity Table) file from the RNAstructure package.
Connect format
Connectivity Table file format
CT
1.3
XRNA old input style format.
SS
1.3
RNA Markup Language.
RNAML
1.3
Format for the Genetic Data Environment (GDE).
GDE
1.3
A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge.
Block file format
BLC
1.3
true
Format of a data index of some type.
Data index format
1.3
BAM indexing format
BAI
1.3
HMMER profile HMM file for HMMER versions 2.x
HMMER2
1.3
HMMER profile HMM file for HMMER versions 3.x
HMMER3
1.3
EMBOSS simple sequence pair alignment format.
PO
1.3
XML format as produced by the NCBI Blast package
BLAST XML results format
1.7
http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf
http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf
Reference-based compression of alignment format
CRAM
1.7
json
JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs.
JavaScript Object Notation
JSON
1.7
Encapsulated PostScript format
EPS
1.7
Graphics Interchange Format.
GIF
1.7
Microsoft Excel spreadsheet format.
Microsoft Excel format
xls
1.7
tsv|tab
Tabular data represented as tab-separated values in a text file.
Tab-delimited
Tab-separated values
TSV
1.7
1.10
Format of a file of gene expression data, e.g. a gene expression matrix or profile.
Gene expression data format
true
1.7
Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments.
Cytoscape input file format
1.7
https://github.com/BenLangmead/bowtie/blob/master/MANUAL
Bowtie format for indexed reference genome for "small" genomes.
Bowtie index format
ebwt
1.7
http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf
Rich sequence format.
GCG RSF
RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual).
RSF
1.7
Some format based on the GCG format.
GCG format variant
1.7
http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc
Bioinformatics Sequence Markup Language format.
BSML
1.7
https://github.com/BenLangmead/bowtie/blob/master/MANUAL
Bowtie format for indexed reference genome for "large" genomes.
Bowtie long index format
ebwtl
1.8
Ensembl standard format for variation data.
Ensembl variation file format
1.8
Microsoft Word format.
Microsoft Word format
doc
docx
1.8
true
Format of documents including word processor, spreadsheet and presentation.
Document format
1.8
Portable Document Format
PDF
1.9
true
Format used for images and image metadata.
Image format
1.9
Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
DICOM format
1.9
Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.
NIfTI-1 format
nii
1.9
Text-based tagged file format for medical images generated using the MetaImage software package.
Metalmage format
mhd
1.9
Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data.
nrrd
1.9
File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics.
R file format
1.9
File format used for scripts for the Statistical Package for the Social Sciences.
SPSS
1.9
mhtml|mht|eml
MHTML is not strictly an HTML format, it is encoded as an HTML email message (although with multipart/related instead of multipart/alternative). It, however, contains the main HTML block as its core, and thus it is for practical reasons incuded in EDAM as a specialisation of 'HTML'.
MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on.
HTML email format
HTML email message format
MHT
MHT format
MHTML format
MIME HTML
MIME HTML format
MIME multipart
MIME multipart format
MIME multipart message
MIME multipart message format
MHTML
1.10
Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array.
IDAT
1.10
Joint Picture Group file format for lossy graphics file.
JPEG
jpeg
Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.
JPG
1.10
Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.
rcc
1.11
ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.
This file format is for machine learning.
arff
1.11
AFG is a single text-based file assembly format that holds read and consensus information together
afg
1.11
The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data
Holds a tab-delimited chromosome /start /end / datavalue dataset.
bedgraph
1.11
Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns.
Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.
bedstrict
1.11
BED file format where each feature is described by chromosome, start, end, name, score, and strand.
Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6
bed6
1.11
A BED file where each feature is described by all twelve columns.
Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12
bed12
1.11
Tabular format of chromosome names and sizes used by Galaxy.
Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.
chrominfo
1.11
Custom Sequence annotation track format used by Galaxy.
Used for tracks/track views within galaxy.
customtrack
1.11
Color space FASTA format sequence variant.
FASTA format extended for color space information.
csfasta
1.11
HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF).
h5
An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj package.
HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF.
HDF5
1.11
A versatile bitmap format.
tiff
The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs.
TIFF
1.11
Standard bitmap storage format in the Microsoft Windows environment.
bmp
Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications.
BMP
1.11
IM is a format used by LabEye and other applications based on the IFUNC image processing library.
IFUNC library reads and writes most uncompressed interchange versions of this format.
im
1.11
Photo CD format, which is the highest resolution format for images on a CD.
PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications.
pcd
1.11
PCX is an image file format that uses a simple form of run-length encoding. It is lossless.
pcx
1.11
The PPM format is a lowest common denominator color image file format.
ppm
1.11
PSD (Photoshop Document) is a proprietary file that allows the user to work with the images' individual layers even after the file has been saved.
psd
1.11
X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI.
The XBM format was replaced by XPM for X11 in 1989.
xbm
1.11
X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels.
Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.
xpm
1.11
RGB file format is the native raster graphics file format for Silicon Graphics workstations.
rgb
1.11
The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters.
pbm
1.11
The PGM format is a lowest common denominator grayscale file format.
It is designed to be extremely easy to learn and write programs for.
pgm
1.11
PNG is a file format for image compression.
It iis expected to replace the Graphics Interchange Format (GIF).
PNG
1.11
Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.
Scalable Vector Graphics
The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.
SVG
1.11
Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems
The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.
rast
1.11
true
Textual report format for sequence quality for reports from sequencing machines.
Sequence quality report format (text)
1.11
http://en.wikipedia.org/wiki/Phred_quality_score
FASTQ format subset for Phred sequencing quality score data only (no sequences).
Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities.
qual
1.11
FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.
Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)
qualsolexa
1.11
http://en.wikipedia.org/wiki/Phred_quality_score
FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.
Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator.
qualillumina
1.11
http://en.wikipedia.org/wiki/Phred_quality_score
FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.
For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format.
qualsolid
1.11
http://en.wikipedia.org/wiki/Phred_quality_score
FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers.
qual454
1.11
Human ENCODE peak format.
Format that covers both the broad peak format and narrow peak format from ENCODE.
ENCODE peak format
1.11
Human ENCODE narrow peak format.
Format that covers both the broad peak format and narrow peak format from ENCODE.
ENCODE narrow peak format
1.11
Human ENCODE broad peak format.
ENCODE broad peak format
1.11
Blocked GNU Zip format.
BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format).
bgzip
1.11
TAB-delimited genome position file index format.
tabix
1.11
true
Data format for graph data.
Graph format
1.11
XML-based format used to store graph descriptions within Galaxy.
xgmml
1.11
SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape.
sif
1.11
MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file.
xlsx
1.11
Data format used by the SQLite database.
SQLite format
1.11
Data format used by the SQLite database conformant to the Gemini schema.
Gemini SQLite format
1.11
Duplicate of http://edamontology.org/format_3326
1.20
Format of a data index of some type.
Index format
true
1.11
An index of a genome database, indexed for use by the snpeff tool.
snpeffdb
1.12
Binary format used by MATLAB files to store workspace variables.
.mat file format
MAT file format
MATLAB file format
MAT
1.12
Network Common Data Form (NetCDF) library is supported by AMBER MD package from version 9.
Format used by netCDF software library for writing and reading chromatography-MS data files. Also used to store trajectory atom coordinates information, such as the ones obtained by Molecular Dynamics simulations.
ANDI-MS
netCDF
1.12
Mascot Generic Format. Encodes multiple MS/MS spectra in a single file.
Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions.
MGF
1.12
Spectral data format file where each spectrum is written to a separate file.
Each file contains one header line for the known or assumed charge and the mass of the precursor peptide ion, calculated from the measured *m*/*z* and the charge. This one line was then followed by all the *m*/*z*, intensity pairs that represent the spectrum.
dta
1.12
Spectral data file similar to dta.
Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to.
pkl
1.12
https://dx.doi.org/10.1038%2Fnbt1031
Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology.
mzXML
1.12
http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd
Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses.
pepXML
1.12
Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways.
GPML
1.12
oxlicg
A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph.
K-mer countgraph
1.13
mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results.
mzTab
1.13
imzML
imzML metadata is a data format for mass spectrometry imaging metadata.
imzML data are recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra. This entry is for the metadata XML file
imzML metadata file
1.13
qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements.
The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well.
qcML
1.13
PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment.
PRIDE XML
1.13
Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements.
SED-ML
1.13
Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology.
An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network).
COMBINE OMEX
1.13
The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from
experiments employing a combination of technologies.
ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model can also be represented in RDF, and in JSON (compliable with a set of defined JSON Schemata).
ISA-TAB
1.13
SBtab is a tabular format for biochemical network models.
SBtab
1.13
Biological Connection Markup Language (BCML) is an XML format for biological pathways.
BCML
1.13
Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics.
BDML
1.13
Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form.
BEL
1.13
SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks.
SBGN-ML
1.13
AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome).
AGP
1.13
PostScript format
PostScript
PS
1.13
SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive.
SRA
SRA archive format
SRA format
1.13
VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive.
SRA native format
VDB
1.13
Index file format used by the samtools package to index TAB-delimited genome position files.
Tabix index file format
1.13
A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries).
Sequin format
1.14
Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software.
Magellan storage file format
This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format.
MSF
1.14
true
Data format for biodiversity data.
Biodiversity data format
1.14
Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data).
ABCD
ABCD format
1.14
Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample.
GCT format
Res format
GCT/Res format
1.14
wiff
Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex).
wiff
WIFF format
1.14
Output format used by X! series search engines that is based on the XML language BIOML.
X!Tandem XML
1.14
Proprietary file format for mass spectrometry data from Thermo Scientific.
Proprietary format for which documentation is not available.
Thermo RAW
1.14
"Raw" result file from Mascot database search.
Mascot .dat file
1.14
Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra.
MaxQuant APL
MaxQuant APL peaklist format
1.14
Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology.
SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs.
SBOL
1.14
PMML uses XML to represent mining models. The structure of the models is described by an XML Schema.
One or more mining models can be contained in a PMML document.
PMML
1.14
Image file format used by the Open Microscopy Environment (OME).
An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical (or in the case of multiple files, nearly identical) string of OME-XML metadata embedded in the ImageDescription tag of each file's first IFD (Image File Directory). BigTIFF file extensions are also permitted, with the file extension .ome.tf2, .ome.tf8 or .ome.btf, but note these file extensions are an addition to the original specification, and software using an older version of the specification may not be able to handle these file extensions.
OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community.
OME-TIFF
1.14
The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record.
Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs.
LocARNA PP
1.14
Input format used by the Database of Genotypes and Phenotypes (dbGaP).
The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH) sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype.
dbGaP format
1.15
biom
The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables.
BIological Observation Matrix format
BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc.
BIOM format
1.15
A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data.
No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML).
protXML
http://doi.org/10.1038/msb4100024
http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v3.xsd
1.15
true
A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries.
Semantic Web format
Linked data format
1.15
jsonld
JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON.
JavaScript Object Notation for Linked Data
JSON-LD
1.15
yaml|yml
YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language.
YAML Ain't Markup Language
Data in YAML format can be serialised into text, or binary format.
YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible".
YAML
1.16
Tabular format
Tabular data represented as values in a text file delimited by some character.
Delimiter-separated values
DSV
1.16
csv
Tabular data represented as comma-separated values in a text file.
Comma-separated values
CSV
1.16
"Raw" result file from SEQUEST database search.
SEQUEST .out file
1.16
http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1IdXMLFile.html
http://open-ms.sourceforge.net/schemas/
XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS.
idXML
1.16
Data table formatted such that it can be passed/streamed within the KNIME platform.
KNIME datatable format
1.16
UniProtKB XML sequence features format is an XML format available for downloading UniProt entries.
UniProt XML
UniProt XML format
UniProtKB XML format
UniProtKB XML
1.16
UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML).
UniProt RDF
UniProt RDF format
UniProtKB RDF format
UniProt RDF/XML
UniProt RDF/XML format
UniProtKB RDF/XML
UniProtKB RDF/XML format
UniProtKB RDF
1.16
Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioJSON' is the JSON format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'.
BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming.
BioJSON (BioXSD data model)
BioJSON format (BioXSD)
BioXSD BioJSON
BioXSD BioJSON format
BioXSD JSON
BioXSD JSON format
BioXSD in JSON
BioXSD in JSON format
BioXSD+JSON
BioXSD/GTrack BioJSON
BioXSD|BioJSON|BioYAML BioJSON
BioXSD|GTrack BioJSON
BioJSON (BioXSD)
1.16
Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioYAML' is the YAML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'.
BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editting, and object-oriented programming.
BioXSD BioYAML
BioXSD BioYAML format
BioXSD YAML
BioXSD YAML format
BioXSD in YAML
BioXSD in YAML format
BioXSD+YAML
BioXSD/GTrack BioYAML
BioXSD|BioJSON|BioYAML BioYAML
BioXSD|GTrack BioYAML
BioYAML (BioXSD data model)
BioYAML (BioXSD)
BioYAML format
BioYAML format (BioXSD)
BioYAML
1.16
BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench.
BioJSON format (Jalview)
JSON (Jalview)
JSON format (Jalview)
Jalview BioJSON
Jalview BioJSON format
Jalview JSON
Jalview JSON format
BioJSON (Jalview)
1.16
'GSuite' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GSuite' is the tabular format for an annotated collection of individual GTrack files.
GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata.
BioXSD/GTrack GSuite
BioXSD|GTrack GSuite
GSuite (GTrack ecosystem of formats)
GSuite format
GTrack|BTrack|GSuite GSuite
GTrack|GSuite|BTrack GSuite
GSuite
1.16
'BTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'BTrack' is the binary, optionally compressed HDF5-based version of the GTrack and GSuite formats.
BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats.
BTrack (GTrack ecosystem of formats)
BTrack format
BioXSD/GTrack BTrack
BioXSD|GTrack BTrack
GTrack|BTrack|GSuite BTrack
GTrack|GSuite|BTrack BTrack
BTrack
1.16
Multi-Crop Passport Descriptors is a format available in 2 successive versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012).
The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information.
Bioversity MCPD
FAO MCPD
MCPD format
Multi-Crop Passport Descriptors
Multi-Crop Passport Descriptors format
IPGRI MCPD
MCPD V.1
MCPD V.2
MCPD
1.16
true
Data format of an annotated text, e.g. with recognised entities, concepts, and relations.
Annotated text format
1.16
JSON format of annotated scientific text used by PubAnnotations and other tools.
PubAnnotation format
1.16
BioC is a standardised XML format for sharing and integrating text data and annotations.
BioC
1.16
Native textual export format of annotated scientific text from PubTator.
PubTator format
1.16
A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD.
Open Annotation format
1.16
A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar.
BRAT format
BRAT standoff format
BioNLP Shared Task format
1.16
true
A query language (format) for structured database queries.
Query format
Query language
1.16
sql
SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases.
Structured Query Language
SQL
1.16
xq|xqy|xquery
XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.).
XML Query
XQuery
1.16
SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format.
SPARQL Protocol and RDF Query Language
SPARQL
1.17
XML format for XML Schema.
xsd
1.20
The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.
alignment format
eXtended Multi-FastA format
XMFA
1.20
The GEN file format contains genetic data and describes SNPs.
Genotype file format
GEN
1.20
The SAMPLE file format contains information about each individual i.e. individual IDs, covariates, phenotypes and missing data proportions, from a GWAS study.
SAMPLE file format
1.20
SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information.
SDF
1.20
An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule.
Molfile
1.20
Complete, portable representation of a SYBYL molecule. ASCII file which contains all the information needed to reconstruct a SYBYL molecule.
Mol2
1.20
format for the LaTeX document preparation system
LaTeX format
uses the TeX typesetting program format
latex
1.20
Tab-delimited text file format used by Eland - the read-mapping program distributed by Illumina with its sequencing analysis pipeline - which maps short Solexa sequence reads to the human reference genome.
ELAND
eland
ELAND format
1.20
Phylip multiple alignment sequence format, less stringent than PHYLIP format.
PHYLIP Interleaved format
It differs from Phylip Format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length.
Relaxed PHYLIP Interleaved
1.20
Phylip multiple alignment sequence format, less stringent than PHYLIP sequential format (format_1998).
Relaxed PHYLIP non-interleaved
Relaxed PHYLIP non-interleaved format
Relaxed PHYLIP sequential format
It differs from Phylip sequential format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length.
Relaxed PHYLIP Sequential
1.20
Default XML format of VisANT, containing all the network information.
VisANT xml
VisANT xml format
VisML
1.20
GML (Graph Modeling Language) is a text file format supporting network data with a very easy syntax. It is used by Graphlet, Pajek, yEd, LEDA and NetworkX.
GML format
GML
1.20
FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty.
FASTG assembly graph format
It is called FASTG, like FASTA, but the G stands for "graph".
FASTG
1.20
true
Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy experiment.
Nuclear magnetic resonance spectroscopy data format
NMR peak assignment data
NMR processed data format
NMR raw data format
Processed NMR data format
Raw NMR data format
NMR data format
1.20
nmrML is an MSI supported XML-based open access format for metabolomics NMR raw and processed spectral data. It is accompanies by an nmrCV (controlled vocabulary) to allow ontology-based annotations.
nmrML
1.20
. proBAM is an adaptation of BAM (format_2572), which was extended to meet specific requirements entailed by proteomics data.
proBAM
1.20
. proBED is an adaptation of BED (format_3003), which was extended to meet specific requirements entailed by proteomics data.
proBED
1.20
true
Data format for raw microarray data.
Microarray data format
Raw microarray data format
1.20
GenePix Results (GPR) text file format developed by Axon Instruments that is used to save GenePix Results data.
GPR
1.20
Binary format used by the ARB software suite
ARB binary format
ARB
1.20
http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1ConsensusXMLFile.html
OpenMS format for grouping features in one map or across several maps.
consensusXML
1.20
http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/classOpenMS_1_1FeatureXMLFile.html
OpenMS format for quantitation results (LC/MS features).
featureXML
1.20
http://www.psidev.info/mzdata-1_0_5-docs
Now deprecated data format of the HUPO Proteomics Standards Initiative. Replaced by mzML (format_3244).
mzData
1.20
http://cruxtoolkit.sourceforge.net/tide-search.html
Format supported by the Tide tool for identifying peptides from tandem mass spectra.
TIDE TXT
1.20
ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/ProposedBLASTXMLChanges.pdf
ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf
http://www.ncbi.nlm.nih.gov/data_specs/schema/NCBI_BlastOutput2.mod.xsd
XML format as produced by the NCBI Blast package v2.
BLAST XML v2 results format
1.20
Microsoft Powerpoint format.
pptx
1.20
ibd
ibd is a data format for mass spectrometry imaging data.
imzML data is recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra.
ibd
1.21
Data format used in Natural Language Processing.
Natural Language Processing format
NLP format
1.21
XML input file format for BEAST Software (Bayesian Evolutionary Analysis Sampling Trees).
BEAST
1.21
Chado-XML format is a direct mapping of the Chado relational schema into XML.
Chado-XML
1.21
An alignment format generated by PRANK/PRANKSTER consisting of four elements: newick, nodes, selection and model.
HSAML
1.21
Output xml file from the InterProScan sequence analysis application.
InterProScan XML
1.21
The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format.
KEGG Markup Language
KGML
1.21
XML format for collected entries from biobliographic databases MEDLINE and PubMed.
MEDLINE XML
PubMed XML
1.21
A set of XML compliant markup components for describing multiple sequence alignments.
MSAML
1.21
OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format.
OrthoXML
1.21
Tree structure of Protein Sequence Database Markup Language generated using Matra software.
PSDML
1.21
SeqXML is an XML Schema to describe biological sequences, developed by the Stockholm Bioinformatics Centre.
SeqXML
1.21
XML format for the UniParc database.
UniParc XML
1.21
XML format for the UniRef reference clusters.
UniRef XML
1.21
cwl
Common Workflow Language (CWL) format for description of command-line tools and workflows.
Common Workflow Language
CommonWL
CWL
1.21
Proprietary file format for mass spectrometry data from Waters.
Proprietary format for which documentation is not available, but used by multiple tools.
Waters RAW
1.21
A standardized file format for data exchange in mass spectrometry, initially developed for infrared spectrometry.
JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression.
JCAMP-DX
1.21
An NLP format used for annotated textual documents.
NLP annotation format
1.21
NLP format used by a specific type of corpus (collection of texts).
NLP corpus format
1.21
mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq workflows.
miRTop format
mirGFF3 is a specialisation of GFF3; produced by small-RNA-Seq analysis workflows, usable and convertible with the miRTop API (https://mirtop.readthedocs.io/en/latest/), and consumable by tools for downstream analysis.
mirGFF3
1.21
RNA data format
A "placeholder" concept for formats of annotated RNA data, including e.g. microRNA and RNA-Seq data.
miRNA data format
microRNA data format
RNA annotation format
1.22
true
File format to store trajectory information for a 3D structure .
CG trajectory formats
MD trajectory formats
NA trajectory formats
Protein trajectory formats
Formats differ on what they are able to store (coordinates, velocities, topologies) and how they are storing it (raw, compressed, textual, binary).
Trajectory format
1.22
true
Binary file format to store trajectory information for a 3D structure .
Trajectory format (binary)
1.22
true
Textual file format to store trajectory information for a 3D structure .
Trajectory format (text)
1.22
HDF is the name of a set of file formats and libraries designed to store and organize large amounts of numerical data, originally developed at the National Center for Supercomputing Applications at the University of Illinois.
HDF is currently supported by many commercial and non-commercial software platforms such as Java, MATLAB/Scilab, Octave, Python and R.
HDF
1.22
PCAZip format is a binary compressed file to store atom coordinates based on Essential Dynamics (ED) and Principal Component Analysis (PCA).
The compression is made projecting the Cartesian snapshots collected along the trajectory into an orthogonal space defined by the most relevant eigenvectors obtained by diagonalization of the covariance matrix (PCA). In the compression/decompression process, part of the original information is lost, depending on the final number of eigenvectors chosen. However, with a reasonable choice of the set of eigenvectors the compression typically reduces the trajectory file to less than one tenth of their original size with very acceptable loss of information. Compression with PCAZip can only be applied to unsolvated structures.
PCAzip
1.22
Portable binary format for trajectories produced by GROMACS package.
XTC uses the External Data Representation (xdr) routines for writing and reading data which were created for the Unix Network File System (NFS). XTC files use a reduced precision (lossy) algorithm which works multiplying the coordinates by a scaling factor (typically 1000), so converting them to pm (GROMACS standard distance unit is nm). This allows an integer rounding of the values. Several other tricks are performed, such as making use of atom proximity information: atoms close in sequence are usually close in space (e.g. water molecules). That makes XTC format the most efficient in terms of disk usage, in most cases reducing by a factor of 2 the size of any other binary trajectory format.
XTC
1.22
Trajectory Next Generation (TNG) is a format for storage of molecular simulation data. It is designed and implemented by the GROMACS development group, and it is called to be the substitute of the XTC format.
Trajectory Next Generation format
TNG
Fully architecture-independent format, regarding both endianness and the ability to mix single/double precision trajectories and I/O libraries. Self-sufficient, it should not require any other files for reading, and all the data should be contained in a single file for easy transport. Temporal compression of data, improving the compression rate of the previous XTC format. Possibility to store meta-data with information about the simulation. Direct access to a particular frame. Efficient parallel I/O.
TNG
1.22
The XYZ chemical file format is widely supported by many programs, although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem XYZ, etc.). Basic information stored for each atom in the system are x, y and z coordinates and atom element/atomic number.
XYZ files are structured in this way: First line contains the number of atoms in the file. Second line contains a title, comment, or filename. Remaining lines contain atom information. Each line starts with the element symbol, followed by x, y and z coordinates in angstroms separated by whitespace. Multiple molecules or frames can be contained within one file, so it supports trajectory storage. XYZ files can be directly represented by a molecular viewer, as they contain all the basic information needed to build the 3D model.
XYZ
1.22
AMBER trajectory (also called mdcrd), with 10 coordinates per line and format F8.3 (fixed point notation with field width 8 and 3 decimal places).
AMBER trajectory format
inpcrd
mdcrd
1.22
true
Format of topology files; containing the static information of a structure molecular system that is needed for a molecular simulation.
CG topology format
MD topology format
NA topology format
Protein topology format
Many different file formats exist describing structural molecular topology. Tipically, each MD package or simulation software works with their own implementation (e.g. GROMACS top, CHARMM psf, AMBER prmtop).
Topology format
1.22
GROMACS MD package top textual files define an entire structure system topology, either directly, or by including itp files.
There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package.
GROMACS top
1.22
AMBER Prmtop file (version 7) is a structure topology text file divided in several sections designed to be parsed easily using simple Fortran code. Each section contains particular topology information, such as atom name, charge, mass, angles, dihedrals, etc.
AMBER Parm
AMBER Parm7
Parm7
Prmtop
Prmtop7
It can be modified manually, but as the size of the system increases, the hand-editing becomes increasingly complex. AMBER Parameter-Topology file format is used extensively by the AMBER software suite and is referred to as the Prmtop file for short.
version 7 is written to distinguish it from old versions of AMBER Prmtop. Similarly to HDF5, it is a completely different format, according to AMBER group: a drastic change to the file format occurred with the 2004 release of Amber 7 (http://ambermd.org/prmtop.pdf)
AMBER top
1.22
X-Plor Protein Structure Files (PSF) are structure topology files used by NAMD and CHARMM molecular simulations programs. PSF files contain six main sections of interest: atoms, bonds, angles, dihedrals, improper dihedrals (force terms used to maintain planarity) and cross-terms.
The high similarity in the functional form of the two potential energy functions used by AMBER and CHARMM force-fields gives rise to the possible use of one force-field within the other MD engine. Therefore, the conversion of PSF files to AMBER Prmtop format is possible with the use of AMBER chamber (CHARMM - AMBER) program.
PSF
1.22
GROMACS itp files (include topology) contain structure topology information, and are tipically included in GROMACS topology files (GROMACS top). Itp files are used to define individual (or multiple) components of a topology as a separate file. This is particularly useful if there is a molecule that is used frequently, and also reduces the size of the system topology file, splitting it in different parts.
GROMACS itp files are used also to define position restrictions on the molecule, or to define the force field parameters for a particular ligand.
GROMACS itp
1.22
Format of force field parameter files, which store the set of parameters (charges, masses, radii, bond lengths, bond dihedrals, etc.) that are essential for the proper description and simulation of a molecular system.
Many different file formats exist describing force field parameters. Tipically, each MD package or simulation software works with their own implementation (e.g. GROMACS itp, CHARMM rtf, AMBER off / frcmod).
FF parameter format
1.22
Scripps Research Institute BinPos format is a binary formatted file to store atom coordinates.
Scripps Research Institute BinPos
It is basically a translation of the ASCII atom coordinate format to binary code. The only additional information stored is a magic number that identifies the BinPos format and the number of atoms per snapshot. The remainder is the chain of coordinates binary encoded. A drawback of this format is its architecture dependency. Integers and floats codification depends on the architecture, thus it needs to be converted if working in different platforms (little endian, big endian).
BinPos
1.22
AMBER coordinate/restart file with 6 coordinates per line and decimal format F12.7 (fixed point notation with field width 12 and 7 decimal places)
restrt
rst7
RST
1.22
Format of CHARMM Residue Topology Files (RTF), which define groups by including the atoms, the properties of the group, and bond and charge information.
There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package.
CHARMM rtf
1.22
AMBER frcmod (Force field Modification) is a file format to store any modification to the standard force field needed for a particular molecule to be properly represented in the simulation.
AMBER frcmod
1.22
AMBER Object File Format library files (OFF library files) store residue libraries (forcefield residue parameters).
AMBER Object File Format
AMBER lib
AMBER off
1.22
MReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or "NMReDATA") includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc.
NMReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or "NMReDATA") includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc. Find more in the paper at D. Jeannerat, Magn. Reson. in Chem., 2017, 55, 7-14.
NMReDATA
1.22
BpForms is a string format for concretely representing the primary structures of biopolymers, including DNA, RNA, and proteins that include non-canonical nucleic and amino acids. See https://www.bpforms.org for more information.
BpForms
1.22
The first 4 bytes of any trr file containing 1993. See https://github.com/galaxyproject/galaxy/pull/6597/files#diff-409951594551183dbf886e24de6cb129R760
Format of trr files that contain the trajectory of a simulation experiment used by GROMACS.
trr
1.22
msh
Mash sketch is a format for sequence / sequence checksum information. To make a sketch, each k-mer in a sequence is hashed, which creates a pseudo-random identifier. By sorting these hashes, a small subset from the top of the sorted list can represent the entire sequence.
Mash sketch
min-hash sketch
msh
1.23
loom
The Loom file format is based on HDF5, a standard for storing large numerical datasets. The Loom format is designed to efficiently hold large omics datasets. Typically, such data takes the form of a large matrix of numbers, along with metadata for the rows and columns.
Loom
1.23
zarray
zgroup
The Zarr format is an implementation of chunked, compressed, N-dimensional arrays for storing data.
Zarr
1.23
mtx
The Matrix Market matrix (MTX) format stores numerical or pattern matrices in a dense (array format) or sparse (coordinate format) representation.
MTX
1.24
text/plain
BcForms is a format for abstractly describing the molecular structure (atoms and bonds) of macromolecular complexes as a collection of subunits and crosslinks. Each subunit can be described with BpForms (http://edamontology.org/format_3909) or SMILES (http://edamontology.org/data_2301). BcForms uses an ontology of crosslinks to abstract the chemical details of crosslinks from the descriptions of complexes (see https://bpforms.org/crosslink.html).
BcForms is related to http://edamontology.org/format_3909. (BcForms uses BpForms to describe subunits which are DNA, RNA, or protein polymers.) However, that format isn't the parent of BcForms. BcForms is similarly related to SMILES (http://edamontology.org/data_2301).
BcForms
1.24
nq
N-Quads is a line-based, plain text format for encoding an RDF dataset. It includes information about the graph each triple belongs to.
N-Quads should not be confused with N-Triples which does not contain graph information.
N-Quads
1.25
json
application/json
Vega is a visualization grammar, a declarative language for creating, saving, and sharing interactive visualization designs. With Vega, you can describe the visual appearance and interactive behavior of a visualization in a JSON format, and generate web-based views using Canvas or SVG.
Vega
1.25
json
application/json
Vega-Lite is a high-level grammar of interactive graphics. It provides a concise JSON syntax for rapidly generating visualizations to support analysis. Vega-Lite specifications can be compiled to Vega specifications.
Vega-lite
1.25
application/xml
A model description language for computational neuroscience.
NeuroML
1.25
bngl
application/xml
plain/text
BioNetGen is a format for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks.
BioNetGen Language
BNGL
1.25
dockerfile
A Docker image is a file, comprised of multiple layers, that is used to execute code in a Docker container. An image is essentially built from the instructions for a complete and executable version of an application, which relies on the host OS kernel.
Docker image format
1.25
gfa
Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology.
GFA 1
1.25
gfa
Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology.
GFA 2
1.25
xlsx
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a syntax for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets.
ObjTables
1.25
contig
The CONTIG format used for output of the SOAPdenovo alignment program. It contains contig sequences generated without using mate pair information.
CONTIG
1.25
wego
WEGO native format used by the Web Gene Ontology Annotation Plot application. Tab-delimited format with gene names and others GO IDs (columns) with one annotation record per line.
WEGO
1.25
rpkm
Tab-delimited format for gene expression levels table, calculated as Reads Per Kilobase per Million (RPKM) mapped reads.
Gene expression levels table format
For example a 1kb transcript with 1000 alignments in a sample of 10 million reads (out of which 8 million reads can be mapped) will have RPKM = 1000/(1 * 8) = 125
RPKM
1.25
tar
TAR archive file format generated by the Unix-based utility tar.
TAR
Tarball
For example a 1kb transcript with 1000 alignments in a sample of 10 million reads (out of which 8 million reads can be mapped) will have RPKM = 1000/(1 * 8) = 125
TAR format
https://en.wikipedia.org/wiki/Tar_(computing)
1.25
chain
The CHAIN format describes a pairwise alignment that allow gaps in both sequences simultaneously and is used by the UCSC Genome Browser.
CHAIN
https://genome.ucsc.edu/goldenPath/help/chain.html
1.25
net
The NET file format is used to describe the data that underlie the net alignment annotations in the UCSC Genome Browser.
NET
https://genome.ucsc.edu/goldenPath/help/net.html
1.25
qmap
Format of QMAP files generated for methylation data from an internal BGI pipeline.
QMAP
1.25
ga
An emerging format for high-level Galaxy workflow description.
Galaxy workflow format
GalaxyWF
gxformat2
https://github.com/galaxyproject/gxformat2
1.25
wmv
The proprietary native video format of various Microsoft programs such as Windows Media Player.
Windows Media Video format
Windows movie file format
WMV
https://en.wikipedia.org/wiki/Windows_Media_Video
1.25
zip
ZIP is an archive file format that supports lossless data compression.
ZIP
A ZIP file may contain one or more files or directories that may have been compressed.
ZIP format
https://en.wikipedia.org/wiki/Zip_(file_format)
1.25
lsm
Zeiss' proprietary image format based on TIFF.
LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings.
LSM
1.25
gz
gzip
GNU zip compressed file format common to Unix-based operating systems.
GNU Zip
GZIP format
https://en.wikipedia.org/wiki/Gzip
1.25
avi
Audio Video Interleaved (AVI) format is a multimedia container format for AVI files, that allows synchronous audio-with-video playback.
Audio Video Interleaved
AVI
https://en.wikipedia.org/wiki/Audio_Video_Interleave
1.25
trackDb
A declaration file format for UCSC browsers track dataset display charateristics.
TrackDB
1.25
cigar
Compact Idiosyncratic Gapped Alignment Report format is a compressed (run-length encoded) pairwise alignment format. It is useful for representing long (e.g. genomic) pairwise alignments.
CIGAR
CIGAR format
http://wiki.bits.vib.be/index.php/CIGAR/
1.25
stl
STL is a file format native to the stereolithography CAD software created by 3D Systems. The format is used to save and share surface-rendered 3D images and also for 3D printing.
stl
Stereolithography format
1.25
u3d
U3D (Universal 3D) is a compressed file format and data structure for 3D computer graphics. It contains 3D model information such as triangle meshes, lighting, shading, motion data, lines and points with color and structure.
Universal 3D
Universal 3D format
U3D
1.25
tex
Bitmap image format used for storing textures.
Texture files can create the appearance of different surfaces and can be applied to both 2D and 3D objects. Note the file extension .tex is also used for LaTex documents which are a completely different format and they are NOT interchangable.
Texture file format
1.25
py
Format for scripts writtenin Python - a widely used high-level programming language for general-purpose programming.
Python
Python program
Python script
1.25
mp4
A digital multimedia container format most commonly used to store video and audio.
MP4
MPEG-4
https://en.wikipedia.org/wiki/Moving_Picture_Experts_Group
1.25
pl
Format for scripts written in Perl - a family of high-level, general-purpose, interpreted, dynamic programming languages.
Perl
Perl program
Perl script
1.25
R
Format for scripts written in the R language - an open source programming language and software environment for statistical computing and graphics that is supported by the R Foundation for Statistical Computing.
R
R program
R script
1.25
Rmd
A file format for making dynamic documents (R Markdown scripts) with the R language.
R markdown
https://rmarkdown.rstudio.com/articles_intro.html
1.25
nii
An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI) commonly used to store brain imaging data obtained using Magnetic Resonance Imaging (MRI) methods.
NIFTI
NIFTI format
1.25
pickle
Format used by Python pickle module for serializing and de-serializing a Python object structure.
pickle
https://docs.python.org/2/library/pickle.html
1.25
npy
The standard binary file format used by NumPy - a fundamental package for scientific computing with Python - for persisting a single arbitrary NumPy array on disk. The format stores all of the shape and dtype information necessary to reconstruct the array correctly.
NumPy
NumPy format
1.25
repz
Format of repertoire (archive) files that can be read by SimToolbox (a MATLAB toolbox for structured illumination fluorescence microscopy) or alternatively extracted with zip file archiver software.
SimTools repertoire file format
https://pdfs.semanticscholar.org/5f25/f1cc6cdf2225fe22dc6fd4fc0296d486a85c.pdf
1.25
cfg
A configuration file used by various programs to store settings that are specific to their respective software.
Configuration file format
1.25
zst
Format used by the Zstandard real-time compression algorith.
Zstandard compression format
Zstandard-compressed file format
Zstandard format
https://github.com/facebook/zstd/blob/master/doc/zstd_compression_format.md
1.25
m
The file format for MATLAB scripts or functions.
MATLAB
MATLAB script
beta12orEarlier
true
Function
A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).
Computational method
Computational operation
Computational procedure
Computational subroutine
Function (programming)
Lambda abstraction
Mathematical function
Mathematical operation
Computational tool
Process
sumo:Function
Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
Operation
http://en.wikipedia.org/wiki/Function_(computer_science)
http://en.wikipedia.org/wiki/Function_(mathematics)
http://en.wikipedia.org/wiki/Subroutine
http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method
http://purl.org/biotop/biotop.owl#Function
http://semanticscience.org/resource/SIO_000017
http://semanticscience.org/resource/SIO_000649
http://wsio.org/operation_001
http://www.ebi.ac.uk/swo/SWO_0000003
http://www.ifomis.org/bfo/1.1/snap#Continuant
http://www.ifomis.org/bfo/1.1/snap#Function
http://www.ifomis.org/bfo/1.1/snap#Quality
http://www.ifomis.org/bfo/1.1/span#Process
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality
http://www.onto-med.de/ontologies/gfo.owl#Function
http://www.onto-med.de/ontologies/gfo.owl#Perpetuant
http://www.onto-med.de/ontologies/gfo.owl#Process
Function
Operation is a function that is computational. It typically has input(s) and output(s), which are always data.
Computational tool
Computational tool provides one or more operations.
Process
Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.
beta12orEarlier
Search or query a data resource and retrieve entries and / or annotation.
Database retrieval
Query
Query and retrieval
beta12orEarlier
beta13
Search database to retrieve all relevant references to a particular entity or entry.
Data retrieval (database cross-reference)
true
beta12orEarlier
true
Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.
This is a broad concept and is used a placeholder for other, more specific concepts.
Annotation
beta12orEarlier
true
Generate an index of (typically a file of) biological data.
Data indexing
Database indexing
Indexing
beta12orEarlier
1.6
Analyse an index of biological data.
Data index analysis
true
beta12orEarlier
beta12orEarlier
Retrieve basic information about a molecular sequence.
Annotation retrieval (sequence)
true
beta12orEarlier
Generate a molecular sequence by some means.
Sequence generation (nucleic acid)
Sequence generation (protein)
Sequence generation
beta12orEarlier
Edit or change a molecular sequence, either randomly or specifically.
Sequence editing
beta12orEarlier
Merge two or more (typically overlapping) molecular sequences.
Sequence splicing
Paired-end merging
Paired-end stitching
Read merging
Read stitching
Sequence merging
beta12orEarlier
Convert a molecular sequence from one type to another.
Sequence conversion
beta12orEarlier
Calculate sequence complexity, for example to find low-complexity regions in sequences.
Sequence complexity calculation
beta12orEarlier
Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.
Sequence ambiguity calculation
beta12orEarlier
Calculate character or word composition or frequency of a molecular sequence.
Sequence composition calculation
beta12orEarlier
Find and/or analyse repeat sequences in (typically nucleotide) sequences.
Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.
Repeat sequence analysis
beta12orEarlier
Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).
Motif discovery
Motifs and patterns might be conserved or over-represented (occur with improbable frequency).
Sequence motif discovery
beta12orEarlier
Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).
Motif scanning
Sequence signature detection
Sequence signature recognition
Motif detection
Motif recognition
Motif search
Sequence motif detection
Sequence motif search
Sequence profile search
Sequence motif recognition
beta12orEarlier
Find motifs shared by molecular sequences.
Sequence motif comparison
beta12orEarlier
beta13
Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.
For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
Transcription regulatory sequence analysis
true
beta12orEarlier
1.19
Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).
Conserved transcription regulatory sequence identification
true
beta12orEarlier
1.18
Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.
Protein property calculation (from structure)
true
beta12orEarlier
Analyse flexibility and motion in protein structure.
CG analysis
MD analysis
Protein Dynamics Analysis
Trajectory analysis
Nucleic Acid Dynamics Analysis
Protein flexibility and motion analysis
Protein flexibility prediction
Protein motion prediction
Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.
Simulation analysis
beta12orEarlier
Identify or screen for 3D structural motifs in protein structure(s).
Protein structural feature identification
Protein structural motif recognition
This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.
Structural motif discovery
beta12orEarlier
Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).
Protein domain recognition
beta12orEarlier
Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).
Protein architecture analysis
beta12orEarlier
WHATIF: SymShellFiveXML
WHATIF: SymShellOneXML
WHATIF: SymShellTenXML
WHATIF: SymShellTwoXML
WHATIF:ListContactsNormal
WHATIF:ListContactsRelaxed
WHATIF:ListSideChainContactsNormal
WHATIF:ListSideChainContactsRelaxed
Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).
Residue interaction calculation
beta12orEarlier
WHATIF:CysteineTorsions
WHATIF:ResidueTorsions
WHATIF:ResidueTorsionsBB
WHATIF:ShowTauAngle
Calculate, visualise or analyse phi/psi angles of a protein structure.
Backbone torsion angle calculation
Cysteine torsion angle calculation
Tau angle calculation
Torsion angle calculation
Protein geometry calculation
beta12orEarlier
Extract, calculate or predict non-positional (physical or chemical) properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence or 3D structure.
Protein property rendering
Protein property calculation (from sequence)
Protein property calculation (from structure)
Protein structural property calculation
Structural property calculation
This includes methods to render and visualise the properties of a protein sequence, and a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
Protein property calculation
beta12orEarlier
Immunogen design
Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.
Antigenicity prediction
Immunogenicity prediction
B cell peptide immunogenicity prediction
Hopp and Woods plotting
MHC peptide immunogenicity prediction
Immunological system are cellular or humoral. In vaccine design to induces a cellular immune response, methods must search for antigens that can be recognized by the major histocompatibility complex (MHC) molecules present in T lymphocytes. If a humoral response is required, antigens for B cells must be identified.
This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot.
This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
Peptide immunogenicity prediction
beta12orEarlier
Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.
Sequence feature prediction
Sequence feature recognition
Motif database search
SO:0000110
Look at "Protein feature detection" (http://edamontology.org/operation_3092) and "Nucleic acid feature detection" (http://edamontology.org/operation_0415) in case more specific terms are needed.
Sequence feature detection
beta12orEarlier
beta13
Extract a sequence feature table from a sequence database entry.
Data retrieval (feature table)
true
beta12orEarlier
1.6
Query the features (in a feature table) of molecular sequence(s).
Feature table query
true
beta12orEarlier
Compare the feature tables of two or more molecular sequences.
Feature comparison
Feature table comparison
Sequence feature comparison
beta12orEarlier
beta13
Display basic information about a sequence alignment.
Data retrieval (sequence alignment)
true
beta12orEarlier
Analyse a molecular sequence alignment.
Sequence alignment analysis
beta12orEarlier
Compare (typically by aligning) two molecular sequence alignments.
See also 'Sequence profile alignment'.
Sequence alignment comparison
beta12orEarlier
Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).
Sequence alignment conversion
beta12orEarlier
beta13
Process (read and / or write) physicochemical property data of nucleic acids.
Nucleic acid property processing
true
beta12orEarlier
Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.
Nucleic acid property calculation
beta12orEarlier
Predict splicing alternatives or transcript isoforms from analysis of sequence data.
Alternative splicing analysis
Alternative splicing detection
Differential splicing analysis
Splice transcript prediction
Alternative splicing prediction
beta12orEarlier
Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects.
Frameshift error detection
Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.
Frameshift detection
beta12orEarlier
Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.
Vector sequence detection
beta12orEarlier
Predict secondary structure of protein sequences.
Secondary structure prediction (protein)
Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.
Protein secondary structure prediction
beta12orEarlier
Predict super-secondary structure of protein sequence(s).
Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
Protein super-secondary structure prediction
beta12orEarlier
Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.
Transmembrane protein prediction
beta12orEarlier
Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions.
Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).
Transmembrane protein analysis
beta12orEarlier
This is a "organisational class" not very useful for annotation per se.
1.19
Predict tertiary structure of a molecular (biopolymer) sequence.
Structure prediction
true
beta12orEarlier
Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.
Residue interaction prediction
Contact map prediction
Protein contact map prediction
Methods usually involve multiple sequence alignment analysis.
Residue contact prediction
beta12orEarlier
1.19
Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
Protein interaction raw data analysis
true
beta12orEarlier
1.12
Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.
Protein-protein interaction prediction (from protein sequence)
true
beta12orEarlier
1.12
Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.
Protein-protein interaction prediction (from protein structure)
true
beta12orEarlier
Analyse a network of protein interactions.
Protein interaction network comparison
Protein interaction network analysis
beta12orEarlier
Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
1.24
Compare two or more biological pathways or networks.
Pathway or network comparison
true
beta12orEarlier
Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).
RNA shape prediction
Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).
RNA secondary structure prediction
beta12orEarlier
Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. For example, compute folding energies such as minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.
Nucleic acid folding
Nucleic acid folding modelling
Nucleic acid folding prediction
Nucleic acid folding energy calculation
Nucleic acid folding analysis
beta12orEarlier
beta13
Retrieve information on restriction enzymes or restriction enzyme sites.
Data retrieval (restriction enzyme annotation)
true
beta12orEarlier
beta13
Identify genetic markers in DNA sequences.
A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.
Genetic marker identification
true
beta12orEarlier
Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances.
Functional mapping
Genetic cartography
Genetic map construction
Genetic map generation
Linkage mapping
QTL mapping
Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.
This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
Genetic mapping
beta12orEarlier
Analyse genetic linkage.
For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.
Linkage analysis
beta12orEarlier
Calculate codon usage statistics and create a codon usage table.
Codon usage table construction
Codon usage table generation
beta12orEarlier
Compare two or more codon usage tables.
Codon usage table comparison
beta12orEarlier
Analyse codon usage in molecular sequences or process codon usage data (e.g. a codon usage table).
Codon usage data analysis
Codon usage table analysis
Codon usage analysis
beta12orEarlier
Identify and plot third base position variability in a nucleotide sequence.
Base position variability plotting
beta12orEarlier
Find exact character or word matches between molecular sequences without full sequence alignment.
Sequence word comparison
beta12orEarlier
Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.
Phylogenetic distance matrix generation
Sequence distance calculation
Sequence distance matrix construction
Sequence distance matrix generation
beta12orEarlier
Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
Sequence redundancy removal
beta12orEarlier
Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
Sequence cluster construction
Sequence cluster generation
The clusters may be output or used internally for some other purpose.
Sequence clustering
beta12orEarlier
Includes methods that align sequence profiles (representing sequence alignments): ethods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'.
Align (identify equivalent sites within) molecular sequences.
Sequence alignment construction
Sequence alignment generation
Consensus-based sequence alignment
Constrained sequence alignment
Multiple sequence alignment (constrained)
Sequence alignment (constrained)
See also "Read mapping"
Sequence alignment
beta12orEarlier
beta13
Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).
Hybrid sequence alignment construction
true
beta12orEarlier
Align molecular sequences using sequence and structural information.
Sequence alignment (structure-based)
Structure-based sequence alignment
beta12orEarlier
Includes methods that align structural (3D) profiles or templates (representing structures or structure alignments) - including methods that perform one-to-one, one-to-many or many-to-many comparisons.
Align (superimpose) molecular tertiary structures.
Structural alignment
3D profile alignment
3D profile-to-3D profile alignment
Structural profile alignment
Structure alignment
beta12orEarlier
Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.
Sequence profile construction
Sequence profile generation
beta12orEarlier
Generate some type of structural (3D) profile or template from a structure or structure alignment.
Structural profile construction
Structural profile generation
3D profile generation
beta12orEarlier
1.19
Align sequence profiles (representing sequence alignments).
Profile-profile alignment
true
beta12orEarlier
1.19
Align structural (3D) profiles or templates (representing structures or structure alignments).
3D profile-to-3D profile alignment
true
beta12orEarlier
Align molecular sequence(s) to sequence profile(s), or profiles to other profiles. A profile typically represents a sequence alignment.
Profile-profile alignment
Profile-to-profile alignment
Sequence-profile alignment
Sequence-to-profile alignment
A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Sequence profile alignment
beta12orEarlier
1.19
Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).
Sequence-to-3D-profile alignment
true
beta12orEarlier
This includes sequence-to-3D-profile alignment methods, which align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment) - methods might perform one-to-one, one-to-many or many-to-many comparisons.
Align molecular sequence to structure in 3D space (threading).
Sequence-structure alignment
Sequence-3D profile alignment
Sequence-to-3D-profile alignment
Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Protein threading
beta12orEarlier
Recognize (predict and identify) known protein structural domains or folds in protein sequence(s) which (typically) are not accompanied by any significant sequence similarity to know structures.
Domain prediction
Fold prediction
Protein domain prediction
Protein fold prediction
Protein fold recognition
Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
Fold recognition
beta12orEarlier
(jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved.
1.17
Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.
This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
Metadata retrieval
true
beta12orEarlier
Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics.
Literature search
beta12orEarlier
Text analysis
Process and analyse text (typically scientific literature) to extract information from it.
Literature mining
Text analytics
Text data mining
Article analysis
Literature analysis
Text mining
beta12orEarlier
Perform in-silico (virtual) PCR.
Virtual PCR
beta12orEarlier
Design or predict oligonucleotide primers for PCR and DNA amplification etc.
PCR primer prediction
Primer design
PCR primer design (based on gene structure)
PCR primer design (for conserved primers)
PCR primer design (for gene transcription profiling)
PCR primer design (for genotyping polymorphisms)
PCR primer design (for large scale sequencing)
PCR primer design (for methylation PCRs)
Primer quality estimation
Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.
This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs.
PCR primer design
beta12orEarlier
Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families.
Microarray probe prediction
Microarray probe design
beta12orEarlier
Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
Metagenomic assembly
Sequence assembly editing
For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
Sequence assembly
beta12orEarlier
1.16
Standardize or normalize microarray data.
Microarray data standardisation and normalisation
true
beta12orEarlier
beta12orEarlier
Process (read and / or write) SAGE, MPSS or SBS experimental data.
Sequencing-based expression profile data processing
true
beta12orEarlier
Perform cluster analysis of expression data to identify groups with similar expression profiles, for example by clustering.
Gene expression clustering
Gene expression profile clustering
Expression profile clustering
beta12orEarlier
The measurement of the activity (expression) of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function.
Feature expression analysis
Functional profiling
Gene expression profile construction
Gene expression profile generation
Gene expression quantification
Gene transcription profiling
Non-coding RNA profiling
Protein profiling
RNA profiling
mRNA profiling
Gene expression profiling generates some sort of gene expression profile, for example from microarray data.
Gene expression profiling
beta12orEarlier
Comparison of expression profiles.
Gene expression comparison
Gene expression profile comparison
Expression profile comparison
beta12orEarlier
beta12orEarlier
Interpret (in functional terms) and annotate gene expression data.
Functional profiling
true
beta12orEarlier
beta12orEarlier
Analyse EST or cDNA sequences.
For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
EST and cDNA sequence analysis
true
beta12orEarlier
beta12orEarlier
Identify and select targets for protein structural determination.
Methods will typically navigate a graph of protein families of known structure.
Structural genomics target selection
true
beta12orEarlier
Includes secondary structure assignment from circular dichroism (CD) spectroscopic data, and from protein coordinate data.
Assign secondary structure from protein coordinate or experimental data.
Protein secondary structure assignment
beta12orEarlier
Assign a protein tertiary structure (3D coordinates), or other aspects of protein structure, from raw experimental data.
NOE assignment
Structure calculation
Protein structure assignment
beta12orEarlier
WHATIF: CorrectedPDBasXML
WHATIF: UseFileDB
WHATIF: UseResidueDB
Evaluate the quality or correctness a protein three-dimensional model.
Protein model validation
Residue validation
Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.
The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
This includes methods that calculate poor quality residues. The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).
Protein structure validation
beta12orEarlier
WHATIF: CorrectedPDBasXML
Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc.
Protein model refinement
Molecular model refinement
beta12orEarlier
Construct a phylogenetic tree.
Phlyogenetic tree construction
Phylogenetic reconstruction
Phylogenetic tree generation
Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.
Phylogenetic inference
beta12orEarlier
Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.
Phylogenetic tree analysis
Phylogenetic modelling
Phylgenetic modelling is the modelling of trait evolution and prediction of trait values using phylogeny as a basis.
Phylogenetic analysis
beta12orEarlier
Compare two or more phylogenetic trees.
For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.
Phylogenetic tree comparison
beta12orEarlier
Edit a phylogenetic tree.
Phylogenetic tree editing
beta12orEarlier
Comparison of a DNA sequence to orthologous sequences in different species and inference of a phylogenetic tree, in order to identify regulatory elements such as transcription factor binding sites (TFBS).
Phylogenetic shadowing
Phylogenetic shadowing is a type of footprinting where many closely related species are used. A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.
Phylogenetic footprinting
beta12orEarlier
1.20
Simulate the folding of a protein.
Protein folding simulation
true
beta12orEarlier
1.19
Predict the folding pathway(s) or non-native structural intermediates of a protein.
Protein folding pathway prediction
true
beta12orEarlier
1.12
Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).
Protein SNP mapping
true
beta12orEarlier
Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.
Variant functional prediction
Protein SNP mapping
Protein mutation modelling
Protein stability change prediction
Protein SNP mapping maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations.
Variant effect prediction
beta12orEarlier
beta12orEarlier
Design molecules that elicit an immune response (immunogens).
Immunogen design
true
beta12orEarlier
1.18
Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
Zinc finger prediction
true
beta12orEarlier
Calculate Km, Vmax and derived data for an enzyme reaction.
Enzyme kinetics calculation
beta12orEarlier
Reformat a file of data (or equivalent entity in memory).
File format conversion
File formatting
File reformatting
Format conversion
Reformatting
Formatting
beta12orEarlier
Test and validate the format and content of a data file.
File format validation
Format validation
beta12orEarlier
true
Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.
Data visualisation
Rendering
Molecular visualisation
Plotting
This includes methods to render and visualise molecules.
Visualisation
beta12orEarlier
Search a sequence database by sequence comparison and retrieve similar sequences.
sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.
This excludes direct retrieval methods (e.g. the dbfetch program).
Sequence database search
beta12orEarlier
Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data.
Structure database search
beta12orEarlier
1.8
Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.
Protein secondary database search
true
beta12orEarlier
1.8
Screen a sequence against a motif or pattern database.
Motif database search
true
beta12orEarlier
1.4
Search a database of sequence profiles with a query sequence.
Sequence profile database search
true
beta12orEarlier
beta12orEarlier
Search a database of transmembrane proteins, for example for sequence or structural similarities.
Transmembrane protein database search
true
beta12orEarlier
1.6
Query a database and retrieve sequences with a given entry code or accession number.
Sequence retrieval (by code)
true
beta12orEarlier
1.6
Query a database and retrieve sequences containing a given keyword.
Sequence retrieval (by keyword)
true
beta12orEarlier
Search a sequence database and retrieve sequences that are similar to a query sequence.
Sequence database search (by sequence)
Structure database search (by sequence)
Sequence similarity search
beta12orEarlier
1.8
Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.
Sequence database search (by motif or pattern)
true
beta12orEarlier
1.6
Search a sequence database and retrieve sequences of a given amino acid composition.
Sequence database search (by amino acid composition)
true
beta12orEarlier
Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property.
Sequence database search (by property)
beta12orEarlier
1.6
Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.
Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.
Sequence database search (by sequence using word-based methods)
true
beta12orEarlier
1.6
Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query.
This includes tools based on PSI-BLAST.
Sequence database search (by sequence using profile-based methods)
true
beta12orEarlier
1.6
Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.
This includes tools based on the Smith-Waterman algorithm or FASTA.
Sequence database search (by sequence using local alignment-based methods)
true
beta12orEarlier
1.6
Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.
This includes tools based on the Needleman and Wunsch algorithm.
Sequence database search (by sequence using global alignment-based methods)
true
beta12orEarlier
1.6
Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.
STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
Sequence database search (by sequence for primer sequences)
true
beta12orEarlier
1.6
Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry.
Sequence database search (by molecular weight)
true
beta12orEarlier
1.6
Search sequence(s) or a sequence database for sequences of a given isoelectric point.
Sequence database search (by isoelectric point)
true
beta12orEarlier
1.6
Query a tertiary structure database and retrieve entries with a given entry code or accession number.
Structure retrieval (by code)
true
beta12orEarlier
1.6
Query a tertiary structure database and retrieve entries containing a given keyword.
Structure retrieval (by keyword)
true
beta12orEarlier
1.8
Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.
Structure database search (by sequence)
true
beta12orEarlier
Search a database of molecular structure and retrieve structures that are similar to a query structure.
Structure database search (by structure)
Structure retrieval by structure
Structural similarity search
beta12orEarlier
Annotate a molecular sequence record with terms from a controlled vocabulary.
Sequence annotation
beta12orEarlier
Annotate a genome sequence with terms from a controlled vocabulary.
Functional genome annotation
Metagenome annotation
Structural genome annotation
Genome annotation
beta12orEarlier
Generate the reverse and / or complement of a nucleotide sequence.
Nucleic acid sequence reverse and complement
Reverse / complement
Reverse and complement
Reverse complement
beta12orEarlier
Generate a random sequence, for example, with a specific character composition.
Random sequence generation
beta12orEarlier
Generate digest fragments for a nucleotide sequence containing restriction sites.
Nucleic acid restriction digest
Restriction digest
beta12orEarlier
This is often followed by calculation of protein fragment masses (http://edamontology.org/operation_0398).
Cleave a protein sequence into peptide fragments (corresponding to enzymatic or chemical cleavage).
Protein sequence cleavage
beta12orEarlier
Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition.
Sequence mutation and randomisation
beta12orEarlier
Mask characters in a molecular sequence (replacing those characters with a mask character).
For example, SNPs or repeats in a DNA sequence might be masked.
Sequence masking
beta12orEarlier
Cut (remove) characters or a region from a molecular sequence.
Sequence cutting
beta12orEarlier
Create (or remove) restriction sites in sequences, for example using silent mutations.
Restriction site creation
beta12orEarlier
Translate a DNA sequence into protein.
DNA translation
beta12orEarlier
Transcribe a nucleotide sequence into mRNA sequence(s).
DNA transcription
beta12orEarlier
1.8
Calculate base frequency or word composition of a nucleotide sequence.
Sequence composition calculation (nucleic acid)
true
beta12orEarlier
1.8
Calculate amino acid frequency or word composition of a protein sequence.
Sequence composition calculation (protein)
true
beta12orEarlier
Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
Repeat sequence detection
beta12orEarlier
Analyse repeat sequence organisation such as periodicity.
Repeat sequence organisation analysis
beta12orEarlier
1.12
Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.
Protein hydropathy calculation (from structure)
true
beta12orEarlier
WHATIF:AtomAccessibilitySolvent
WHATIF:AtomAccessibilitySolventPlus
Calculate solvent accessible or buried surface areas in protein or other molecular structures.
Protein solvent accessibility calculation
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
Accessible surface calculation
beta12orEarlier
1.12
Identify clusters of hydrophobic or charged residues in a protein structure.
Protein hydropathy cluster calculation
true
beta12orEarlier
Calculate whether a protein structure has an unusually large net charge (dipole moment).
Protein dipole moment calculation
beta12orEarlier
WHATIF:AtomAccessibilityMolecular
WHATIF:AtomAccessibilityMolecularPlus
WHATIF:ResidueAccessibilityMolecular
WHATIF:ResidueAccessibilitySolvent
WHATIF:ResidueAccessibilityVacuum
WHATIF:ResidueAccessibilityVacuumMolecular
WHATIF:TotAccessibilityMolecular
WHATIF:TotAccessibilitySolvent
Calculate the molecular surface area in proteins and other macromolecules.
Protein atom surface calculation
Protein residue surface calculation
Protein surface and interior calculation
Protein surface calculation
Molecular surface calculation
beta12orEarlier
1.12
Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.
Protein binding site prediction (from structure)
true
beta12orEarlier
Analyse the interaction of protein with nucleic acids, e.g. RNA or DNA-binding sites, interfaces etc.
Protein-nucleic acid binding site analysis
Protein-DNA interaction analysis
Protein-RNA interaction analysis
Protein-nucleic acid interaction analysis
beta12orEarlier
Decompose a structure into compact or globular fragments (protein peeling).
Protein peeling
beta12orEarlier
Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.
Protein distance matrix calculation
beta12orEarlier
Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.
Protein contact map calculation
Contact map calculation
beta12orEarlier
Calculate clusters of contacting residues in protein structures.
This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role.
Residue cluster calculation
beta12orEarlier
WHATIF:HasHydrogenBonds
WHATIF:ShowHydrogenBonds
WHATIF:ShowHydrogenBondsM
Identify potential hydrogen bonds between amino acids and other groups.
The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.
Hydrogen bond calculation
beta12orEarlier
1.12
Calculate non-canonical atomic interactions in protein structures.
Residue non-canonical interaction detection
true
beta12orEarlier
Calculate a Ramachandran plot of a protein structure.
Ramachandran plot calculation
beta12orEarlier
1.22
Validate a Ramachandran plot of a protein structure.
Ramachandran plot validation
true
beta12orEarlier
Calculate the molecular weight of a protein sequence or fragments.
Peptide mass calculation
Protein molecular weight calculation
beta12orEarlier
Predict extinction coefficients or optical density of a protein sequence.
Protein extinction coefficient calculation
beta12orEarlier
Calculate pH-dependent properties from pKa calculations of a protein sequence.
Protein pH-dependent property calculation
Protein pKa calculation
beta12orEarlier
1.12
Hydropathy calculation on a protein sequence.
Protein hydropathy calculation (from sequence)
true
beta12orEarlier
Plot a protein titration curve.
Protein titration curve plotting
beta12orEarlier
Calculate isoelectric point of a protein sequence.
Protein isoelectric point calculation
beta12orEarlier
Estimate hydrogen exchange rate of a protein sequence.
Protein hydrogen exchange rate calculation
beta12orEarlier
Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.
Protein hydrophobic region calculation
beta12orEarlier
Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.
Protein aliphatic index calculation
beta12orEarlier
Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.
Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
Protein hydrophobic moment plotting
beta12orEarlier
Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc.
Protein globularity prediction
beta12orEarlier
Predict the solubility or atomic solvation energy of a protein sequence.
Protein solubility prediction
beta12orEarlier
Predict crystallizability of a protein sequence.
Protein crystallizability prediction
beta12orEarlier
(jison)Too fine-grained.
1.17
Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins.
Protein signal peptide detection (eukaryotes)
true
beta12orEarlier
(jison)Too fine-grained.
1.17
Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins.
Protein signal peptide detection (bacteria)
true
beta12orEarlier
1.12
Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.
MHC peptide immunogenicity prediction
true
beta12orEarlier
1.6
Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.
Methods typically involve scanning for known motifs, patterns and regular expressions.
Protein feature prediction (from sequence)
true
beta12orEarlier
Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.
Sequence feature detection (nucleic acid)
Nucleic acid feature prediction
Nucleic acid feature recognition
Nucleic acid site detection
Nucleic acid site prediction
Nucleic acid site recognition
Methods typically involve scanning for known motifs, patterns and regular expressions.
This is placeholder but does not comprehensively include all child concepts - please inspect other concepts under "Nucleic acid sequence analysis" for example "Gene prediction", for other feature detection operations.
Nucleic acid feature detection
beta12orEarlier
Predict antigenic determinant sites (epitopes) in protein sequences.
Antibody epitope prediction
Epitope prediction
B cell epitope mapping
B cell epitope prediction
Epitope mapping (MHC Class I)
Epitope mapping (MHC Class II)
T cell epitope mapping
T cell epitope prediction
Epitope mapping is commonly done during vaccine design.
Epitope mapping
beta12orEarlier
Predict post-translation modification sites in protein sequences.
PTM analysis
PTM prediction
PTM site analysis
Post-translation modification site prediction
Post-translational modification analysis
Post-translational modification site prediction
Protein post-translation modification site prediction
Acetylation prediction
Acetylation site prediction
Dephosphorylation prediction
Dephosphorylation site prediction
GPI anchor prediction
GPI anchor site prediction
GPI modification prediction
GPI modification site prediction
Glycosylation prediction
Glycosylation site prediction
Hydroxylation prediction
Hydroxylation site prediction
Methylation prediction
Methylation site prediction
N-myristoylation prediction
N-myristoylation site prediction
N-terminal acetylation prediction
N-terminal acetylation site prediction
N-terminal myristoylation prediction
N-terminal myristoylation site prediction
Palmitoylation prediction
Palmitoylation site prediction
Phosphoglycerylation prediction
Phosphoglycerylation site prediction
Phosphorylation prediction
Phosphorylation site prediction
Phosphosite localization
Prenylation prediction
Prenylation site prediction
Pupylation prediction
Pupylation site prediction
S-nitrosylation prediction
S-nitrosylation site prediction
S-sulfenylation prediction
S-sulfenylation site prediction
Succinylation prediction
Succinylation site prediction
Sulfation prediction
Sulfation site prediction
Sumoylation prediction
Sumoylation site prediction
Tyrosine nitration prediction
Tyrosine nitration site prediction
Ubiquitination prediction
Ubiquitination site prediction
Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.
PTM site prediction
beta12orEarlier
Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.
Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
Protein signal peptide detection
beta12orEarlier
1.12
Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.
Protein binding site prediction (from sequence)
true
beta12orEarlier
Predict or detect RNA and DNA-binding binding sites in protein sequences.
Protein-nucleic acid binding detection
Protein-nucleic acid binding prediction
Protein-nucleic acid binding site detection
Protein-nucleic acid binding site prediction
Zinc finger prediction
This includes methods that predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
Nucleic acids-binding site prediction
beta12orEarlier
1.20
Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation.
Protein folding site prediction
true
beta12orEarlier
Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.
Protein cleavage site prediction
beta12orEarlier
1.8
Predict epitopes that bind to MHC class I molecules.
Epitope mapping (MHC Class I)
true
beta12orEarlier
1.8
Predict epitopes that bind to MHC class II molecules.
Epitope mapping (MHC Class II)
true
beta12orEarlier
1.12
Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.
Whole gene prediction
true
beta12orEarlier
1.12
Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.
Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
Gene component prediction
true
beta12orEarlier
Detect or predict transposons, retrotransposons / retrotransposition signatures etc.
Transposon prediction
beta12orEarlier
Detect polyA signals in nucleotide sequences.
PolyA detection
PolyA prediction
PolyA signal prediction
Polyadenylation signal detection
Polyadenylation signal prediction
PolyA signal detection
beta12orEarlier
Detect quadruplex-forming motifs in nucleotide sequences.
Quadruplex structure prediction
Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.
Quadruplex formation site detection
beta12orEarlier
Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.
CpG island and isochores detection
CpG island and isochores rendering
An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.
CpG island and isochore detection
beta12orEarlier
Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.
Restriction site recognition
beta12orEarlier
Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.
Nucleosome exclusion sequence prediction
Nucleosome formation sequence prediction
Nucleosome position prediction
beta12orEarlier
Identify, predict or analyse splice sites in nucleotide sequences.
Splice prediction
Methods might require a pre-mRNA or genomic DNA sequence.
Splice site prediction
beta12orEarlier
1.19
Predict whole gene structure using a combination of multiple methods to achieve better predictions.
Integrated gene prediction
true
beta12orEarlier
Find operons (operators, promoters and genes) in bacteria genes.
Operon prediction
beta12orEarlier
Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.
ORF finding
ORF prediction
Coding region prediction
beta12orEarlier
Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.
Selenocysteine insertion sequence (SECIS) prediction
SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.
SECIS element prediction
beta12orEarlier
This includes comparative genomics approaches that identify common, conserved (homologous) or synonymous transcriptional regulatory elements. For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.
Identify or predict transcriptional regulatory motifs, patterns, elements or regions in DNA sequences.
Regulatory element prediction
Transcription regulatory element prediction
Conserved transcription regulatory sequence identification
Translational regulatory element prediction
This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.
Transcriptional regulatory element prediction
beta12orEarlier
Predict translation initiation sites, possibly by searching a database of sites.
Translation initiation site prediction
beta12orEarlier
Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences.
Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.
Promoter prediction
beta12orEarlier
Identify, predict or analyse cis-regulatory elements in DNA sequences (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) or in RNA sequences (e.g. riboswitches).
Transcriptional regulatory element prediction (DNA-cis)
Transcriptional regulatory element prediction (RNA-cis)
Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand from which the element was transcribed. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. They also occur in RNA sequences, e.g. a riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
cis-regulatory element prediction
beta12orEarlier
1.19
Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.
Transcriptional regulatory element prediction (RNA-cis)
true
beta12orEarlier
Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.
Functional RNA identification
Transcriptional regulatory element prediction (trans)
Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.
trans-regulatory element prediction
beta12orEarlier
Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.
MAR/SAR prediction
Matrix/scaffold attachment site prediction
MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.
S/MAR prediction
beta12orEarlier
Identify or predict transcription factor binding sites in DNA sequences.
Transcription factor binding site prediction
beta12orEarlier
Identify or predict exonic splicing enhancers (ESE) in exons.
An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.
Exonic splicing enhancer prediction
beta12orEarlier
Evaluate molecular sequence alignment accuracy.
Sequence alignment quality evaluation
Evaluation might be purely sequence-based or use structural information.
Sequence alignment validation
beta12orEarlier
Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.
Residue conservation analysis
Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.
Sequence alignment analysis (conservation)
beta12orEarlier
Analyse correlations between sites in a molecular sequence alignment.
This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.
Sequence alignment analysis (site correlation)
beta12orEarlier
Detects chimeric sequences (chimeras) from a sequence alignment.
Chimeric sequence detection
A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.
Chimera detection
beta12orEarlier
Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.
Sequence alignment analysis (recombination detection)
Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
Recombination detection
beta12orEarlier
Identify insertion, deletion and duplication events from a sequence alignment.
Indel discovery
Sequence alignment analysis (indel detection)
Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
Indel detection
beta12orEarlier
beta12orEarlier
Predict nucleosome formation potential of DNA sequences.
Nucleosome formation potential prediction
true
beta12orEarlier
Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy.
Nucleic acid thermodynamic property calculation
beta12orEarlier
Calculate and plot a DNA or DNA/RNA melting profile.
A melting profile is used to visualise and analyse partly melted DNA conformations.
Nucleic acid melting profile plotting
beta12orEarlier
Calculate and plot a DNA or DNA/RNA stitch profile.
A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.
Nucleic acid stitch profile plotting
beta12orEarlier
Calculate and plot a DNA or DNA/RNA melting curve.
Nucleic acid melting curve plotting
beta12orEarlier
Calculate and plot a DNA or DNA/RNA probability profile.
Nucleic acid probability profile plotting
beta12orEarlier
Calculate and plot a DNA or DNA/RNA temperature profile.
Nucleic acid temperature profile plotting
beta12orEarlier
Calculate curvature and flexibility / stiffness of a nucleotide sequence.
This includes properties such as.
Nucleic acid curvature calculation
beta12orEarlier
Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence.
miRNA prediction
microRNA detection
microRNA target detection
miRNA target prediction
beta12orEarlier
Identify or predict tRNA genes in genomic sequences (tRNA).
tRNA gene prediction
beta12orEarlier
Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences.
siRNA binding specificity prediction
beta12orEarlier
1.18
Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.
Protein secondary structure prediction (integrated)
true
beta12orEarlier
Predict helical secondary structure of protein sequences.
Protein secondary structure prediction (helices)
beta12orEarlier
Predict turn structure (for example beta hairpin turns) of protein sequences.
Protein secondary structure prediction (turns)
beta12orEarlier
Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.
Protein secondary structure prediction (coils)
beta12orEarlier
Predict cysteine bonding state and disulfide bond partners in protein sequences.
Disulfide bond prediction
beta12orEarlier
Not sustainable to have protein type-specific concepts.
1.19
Predict G protein-coupled receptors (GPCR).
GPCR prediction
true
beta12orEarlier
Not sustainable to have protein type-specific concepts.
1.19
Analyse G-protein coupled receptor proteins (GPCRs).
GPCR analysis
true
beta12orEarlier
This includes methods that predict the folding pathway(s) or non-native structural intermediates of a protein.
Predict tertiary structure (backbone and side-chain conformation) of protein sequences.
Protein folding pathway prediction
Protein structure prediction
beta12orEarlier
Predict structure of DNA or RNA.
Methods might identify thermodynamically stable or evolutionarily conserved structures.
Nucleic acid structure prediction
beta12orEarlier
Predict tertiary structure of protein sequence(s) without homologs of known structure.
de novo structure prediction
Ab initio structure prediction
beta12orEarlier
Build a three-dimensional protein model based on known (for example homologs) structures.
Comparative modelling
Homology modelling
Homology structure modelling
Protein structure comparative modelling
The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc.
Protein modelling
beta12orEarlier
Model the structure of a protein in complex with a small molecule or another macromolecule.
Docking simulation
Macromolecular docking
This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.
Molecular docking
beta12orEarlier
Model protein backbone conformation.
Protein modelling (backbone)
Design optimization
Epitope grafting
Scaffold search
Scaffold selection
Methods might require a preliminary C(alpha) trace.
Scaffold selection, scaffold search, epitope grafting and design optimization are stages of backbone modelling done during rational vaccine design.
Backbone modelling
beta12orEarlier
Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.
Protein modelling (side chains)
Antibody optimisation
Antigen optimisation
Antigen resurfacing
Rotamer likelihood prediction
Antibody optimisation is to optimize the antibody-interacting surface of the antigen (epitope). Antigen optimisation is to optimize the antigen-interacting surface of the antibody (paratope). Antigen resurfacing is to resurface the antigen by varying the sequence of non-epitope regions.
Methods might use a residue rotamer library.
This includes rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
Side chain modelling
beta12orEarlier
Model loop conformation in protein structures.
Protein loop modelling
Protein modelling (loops)
Loop modelling
beta12orEarlier
Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.
Ligand-binding simulation
Protein-peptide docking
Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.
Virtual screening is used in drug discovery to search libraries of small molecules in order to identify those molecules which are most likely to bind to a drug target (typically a protein receptor or enzyme).
Protein-ligand docking
beta12orEarlier
Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.
Nucleic acid folding family identification
Structured RNA prediction and optimisation
RNA inverse folding
beta12orEarlier
Find single nucleotide polymorphisms (SNPs) - single nucleotide change in base positions - between sequences. Typically done for sequences from a high-throughput sequencing experiment that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.
SNP calling
SNP discovery
Single nucleotide polymorphism detection
This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.
SNP detection
beta12orEarlier
Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers.
Radiation Hybrid Mapping
beta12orEarlier
beta12orEarlier
Map the genetic architecture of dynamic complex traits.
This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
Functional mapping
true
beta12orEarlier
Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.
Haplotype inference
Haplotype map generation
Haplotype reconstruction
Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
Haplotype mapping
beta12orEarlier
Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.
Linkage disequilibrium calculation
beta12orEarlier
Predict genetic code from analysis of codon usage data.
Genetic code prediction
beta12orEarlier
Render a representation of a distribution that consists of group of data points plotted on a simple scale.
Categorical plot plotting
Dotplot plotting
Dot plots are useful when having not too many (e.g. 20) data points for each category. Example: draw a dotplot of sequence similarities identified from word-matching or character comparison.
Dot plot plotting
beta12orEarlier
Align exactly two molecular sequences.
Pairwise alignment
Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Pairwise sequence alignment
beta12orEarlier
Align more than two molecular sequences.
Multiple alignment
This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.
Multiple sequence alignment
beta12orEarlier
1.6
Locally align exactly two molecular sequences.
Local alignment methods identify regions of local similarity.
Pairwise sequence alignment generation (local)
true
beta12orEarlier
1.6
Globally align exactly two molecular sequences.
Global alignment methods identify similarity across the entire length of the sequences.
Pairwise sequence alignment generation (global)
true
beta12orEarlier
Locally align two or more molecular sequences.
Local sequence alignment
Sequence alignment (local)
Smith-Waterman
Local alignment methods identify regions of local similarity.
Local alignment
beta12orEarlier
Globally align two or more molecular sequences.
Global sequence alignment
Sequence alignment (global)
Global alignment methods identify similarity across the entire length of the sequences.
Global alignment
beta12orEarlier
1.19
Align two or more molecular sequences with user-defined constraints.
Constrained sequence alignment
true
beta12orEarlier
1.16
Align two or more molecular sequences using multiple methods to achieve higher quality.
Consensus-based sequence alignment
true
beta12orEarlier
Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.
Multiple sequence alignment (phylogenetic tree-based)
Multiple sequence alignment construction (phylogenetic tree-based)
Phylogenetic tree-based multiple sequence alignment construction
Sequence alignment (phylogenetic tree-based)
Sequence alignment generation (phylogenetic tree-based)
This is supposed to give a more biologically meaningful alignment than standard alignments.
Tree-based sequence alignment
beta12orEarlier
1.6
Align molecular secondary structure (represented as a 1D string).
Secondary structure alignment generation
true
beta12orEarlier
1.18
Align protein secondary structures.
Protein secondary structure alignment generation
true
beta12orEarlier
Align RNA secondary structures.
RNA secondary structure alignment construction
RNA secondary structure alignment generation
Secondary structure alignment (RNA)
RNA secondary structure alignment
beta12orEarlier
Align (superimpose) exactly two molecular tertiary structures.
Structure alignment (pairwise)
Pairwise protein structure alignment
Pairwise structure alignment
beta12orEarlier
Align (superimpose) more than two molecular tertiary structures.
Structure alignment (multiple)
Multiple protein structure alignment
This includes methods that use an existing alignment.
Multiple structure alignment
beta12orEarlier
beta13
Align protein tertiary structures.
Structure alignment (protein)
true
beta12orEarlier
beta13
Align RNA tertiary structures.
Structure alignment (RNA)
true
beta12orEarlier
1.6
Locally align (superimpose) exactly two molecular tertiary structures.
Local alignment methods identify regions of local similarity, common substructures etc.
Pairwise structure alignment generation (local)
true
beta12orEarlier
1.6
Globally align (superimpose) exactly two molecular tertiary structures.
Global alignment methods identify similarity across the entire structures.
Pairwise structure alignment generation (global)
true
beta12orEarlier
Locally align (superimpose) two or more molecular tertiary structures.
Structure alignment (local)
Local protein structure alignment
Local alignment methods identify regions of local similarity, common substructures etc.
Local structure alignment
beta12orEarlier
Globally align (superimpose) two or more molecular tertiary structures.
Structure alignment (global)
Global protein structure alignment
Global alignment methods identify similarity across the entire structures.
Global structure alignment
beta12orEarlier
1.16
Align exactly two molecular profiles.
Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Profile-profile alignment (pairwise)
true
beta12orEarlier
1.6
Align two or more molecular profiles.
Sequence alignment generation (multiple profile)
true
beta12orEarlier
1.16
Align exactly two molecular Structural (3D) profiles.
3D profile-to-3D profile alignment (pairwise)
true
beta12orEarlier
1.6
Align two or more molecular 3D profiles.
Structural profile alignment generation (multiple)
true
beta12orEarlier
1.6
Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.
Data retrieval (tool metadata)
true
beta12orEarlier
1.6
Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.
Data retrieval (database metadata)
true
beta12orEarlier
1.13
Predict primers for large scale sequencing.
PCR primer design (for large scale sequencing)
true
beta12orEarlier
1.13
Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).
PCR primer design (for genotyping polymorphisms)
true
beta12orEarlier
1.13
Predict primers for gene transcription profiling.
PCR primer design (for gene transcription profiling)
true
beta12orEarlier
1.13
Predict primers that are conserved across multiple genomes or species.
PCR primer design (for conserved primers)
true
beta12orEarlier
1.13
Predict primers based on gene structure.
PCR primer design (based on gene structure)
true
beta12orEarlier
1.13
Predict primers for methylation PCRs.
PCR primer design (for methylation PCRs)
true
beta12orEarlier
Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome.
Sequence assembly (mapping assembly)
The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.
Mapping assembly
beta12orEarlier
Sequence assembly by combining fragments without the aid of a reference sequence or genome.
De Bruijn graph
Sequence assembly (de-novo assembly)
De-novo assemblers are much slower and more memory intensive than mapping assemblers.
De-novo assembly
beta12orEarlier
The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated.
Genomic assembly
Sequence assembly (genome assembly)
Breakend assembly
Genome assembly
beta12orEarlier
Sequence assembly for EST sequences (transcribed mRNA).
Sequence assembly (EST assembly)
Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.
EST assembly
beta12orEarlier
Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data.
Tag to gene assignment
Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome.
Sequence tag mapping
beta12orEarlier
beta12orEarlier
Process (read and / or write) serial analysis of gene expression (SAGE) data.
SAGE data processing
true
beta12orEarlier
beta12orEarlier
Process (read and / or write) massively parallel signature sequencing (MPSS) data.
MPSS data processing
true
beta12orEarlier
beta12orEarlier
Process (read and / or write) sequencing by synthesis (SBS) data.
SBS data processing
true
beta12orEarlier
Generate a heat map of expression data from e.g. microarray data.
Heat map construction
Heatmap generation
The heat map usually uses a coloring scheme to represent expression values. They can show how quantitative measurements were influenced by experimental conditions.
Heat map generation
beta12orEarlier
1.6
Analyse one or more gene expression profiles, typically to interpret them in functional terms.
Gene expression profile analysis
true
beta12orEarlier
Map an expression profile to known biological pathways, for example, to identify or reconstruct a pathway.
Pathway mapping
Gene expression profile pathway mapping
Gene to pathway mapping
Gene-to-pathway mapping
Expression profile pathway mapping
beta12orEarlier
1.18
Assign secondary structure from protein coordinate data.
Protein secondary structure assignment (from coordinate data)
true
beta12orEarlier
1.18
Assign secondary structure from circular dichroism (CD) spectroscopic data.
Protein secondary structure assignment (from CD data)
true
beta12orEarlier
1.7
Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.
Protein structure assignment (from X-ray crystallographic data)
true
beta12orEarlier
1.7
Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.
Protein structure assignment (from NMR data)
true
beta12orEarlier
true
Construct a phylogenetic tree from a specific type of data.
Phylogenetic tree construction (data centric)
Phylogenetic tree generation (data centric)
Subconcepts of this concept reflect different types of data used to generate a tree, and provide an alternate axis for curation.
Phylogenetic inference (data centric)
beta12orEarlier
true
Construct a phylogenetic tree using a specific method.
Phylogenetic tree construction (method centric)
Phylogenetic tree generation (method centric)
Subconcepts of this concept reflect different computational methods used to generate a tree, and provide an alternate axis for curation.
Phylogenetic inference (method centric)
beta12orEarlier
Phylogenetic tree construction from molecular sequences.
Phylogenetic tree construction (from molecular sequences)
Phylogenetic tree generation (from molecular sequences)
Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.
Phylogenetic inference (from molecular sequences)
beta12orEarlier
Phylogenetic tree construction from continuous quantitative character data.
Phylogenetic tree construction (from continuous quantitative characters)
Phylogenetic tree generation (from continuous quantitative characters)
Phylogenetic inference (from continuous quantitative characters)
beta12orEarlier
Phylogenetic tree construction from gene frequency data.
Phylogenetic tree construction (from gene frequencies)
Phylogenetic tree generation (from gene frequencies)
Phylogenetic inference (from gene frequencies)
beta12orEarlier
Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data.
Phylogenetic tree construction (from polymorphism data)
Phylogenetic tree generation (from polymorphism data)
Phylogenetic inference (from polymorphism data)
beta12orEarlier
Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.
Phylogenetic species tree construction
Phylogenetic species tree generation
Species tree construction
beta12orEarlier
Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment.
Phylogenetic tree construction (parsimony methods)
Phylogenetic tree generation (parsimony methods)
This includes evolutionary parsimony (invariants) methods.
Phylogenetic inference (parsimony methods)
beta12orEarlier
Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.
Phylogenetic tree construction (minimum distance methods)
Phylogenetic tree generation (minimum distance methods)
This includes neighbor joining (NJ) clustering method.
Phylogenetic inference (minimum distance methods)
beta12orEarlier
Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.
Phylogenetic tree construction (maximum likelihood and Bayesian methods)
Phylogenetic tree generation (maximum likelihood and Bayesian methods)
Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.
Phylogenetic inference (maximum likelihood and Bayesian methods)
beta12orEarlier
Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.
Phylogenetic tree construction (quartet methods)
Phylogenetic tree generation (quartet methods)
Phylogenetic inference (quartet methods)
beta12orEarlier
Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.
Phylogenetic tree construction (AI methods)
Phylogenetic tree generation (AI methods)
Phylogenetic inference (AI methods)
beta12orEarlier
Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment.
Nucleotide substitution modelling
DNA substitution modelling
beta12orEarlier
Analyse the shape (topology) of a phylogenetic tree.
Phylogenetic tree analysis (shape)
Phylogenetic tree topology analysis
beta12orEarlier
Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.
Phylogenetic tree bootstrapping
beta12orEarlier
Construct a "gene tree" which represents the evolutionary history of the genes included in the study. This can be used to predict families of genes and gene function based on their position in a phylogenetic tree.
Phylogenetic tree analysis (gene family prediction)
Gene trees can provide evidence for gene duplication events, as well as speciation events. Where sequences from different homologs are included in a gene tree, subsequent clustering of the orthologs can demonstrate evolutionary history of the orthologs.
Gene tree construction
beta12orEarlier
Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive).
Phylogenetic tree analysis (natural selection)
Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.
Allele frequency distribution analysis
beta12orEarlier
Compare two or more phylogenetic trees to produce a consensus tree.
Phylogenetic tree construction (consensus)
Phylogenetic tree generation (consensus)
Methods typically test for topological similarity between trees using for example a congruence index.
Consensus tree construction
beta12orEarlier
Compare two or more phylogenetic trees to detect subtrees or supertrees.
Phylogenetic sub/super tree detection
Subtree construction
Supertree construction
Phylogenetic sub/super tree construction
beta12orEarlier
Compare two or more phylogenetic trees to calculate distances between trees.
Phylogenetic tree distances calculation
beta12orEarlier
Annotate a phylogenetic tree with terms from a controlled vocabulary.
Phylogenetic tree annotation
http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation
beta12orEarlier
1.12
Predict and optimise peptide ligands that elicit an immunological response.
Immunogenicity prediction
true
beta12orEarlier
Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.
DNA vaccine design
beta12orEarlier
1.12
Reformat (a file or other report of) molecular sequence(s).
Sequence formatting
true
beta12orEarlier
1.12
Reformat (a file or other report of) molecular sequence alignment(s).
Sequence alignment formatting
true
beta12orEarlier
1.12
Reformat a codon usage table.
Codon usage table formatting
true
beta12orEarlier
Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown.
Sequence rendering
Sequence alignment visualisation
Sequence visualisation
beta12orEarlier
1.15
Visualise, format or print a molecular sequence alignment.
Sequence alignment visualisation
true
beta12orEarlier
Visualise, format or render sequence clusters.
Sequence cluster rendering
Sequence cluster visualisation
beta12orEarlier
Render or visualise a phylogenetic tree.
Phylogenetic tree rendering
Phylogenetic tree visualisation
beta12orEarlier
1.15
Visualise RNA secondary structure, knots, pseudoknots etc.
RNA secondary structure visualisation
true
beta12orEarlier
1.15
Render and visualise protein secondary structure.
Protein secondary structure visualisation
true
beta12orEarlier
Visualise or render molecular 3D structure, for example a high-quality static picture or animation.
Structure rendering
Protein secondary structure visualisation
RNA secondary structure visualisation
This includes visualisation of protein secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure.
Structure visualisation
beta12orEarlier
Visualise microarray or other expression data.
Expression data rendering
Gene expression data visualisation
Microarray data rendering
Expression data visualisation
beta12orEarlier
1.19
Identify and analyse networks of protein interactions.
Protein interaction network visualisation
true
beta12orEarlier
Draw or visualise a DNA map.
DNA map drawing
Map rendering
Map drawing
beta12orEarlier
beta12orEarlier
Render a sequence with motifs.
Sequence motif rendering
true
beta12orEarlier
Draw or visualise restriction maps in DNA sequences.
Restriction map drawing
beta12orEarlier
beta12orEarlier
Draw a linear maps of DNA.
DNA linear map rendering
true
beta12orEarlier
DNA circular map rendering
Draw a circular maps of DNA, for example a plasmid map.
Plasmid map drawing
beta12orEarlier
Visualise operon structure etc.
Operon rendering
Operon drawing
beta12orEarlier
beta12orEarlier
Identify folding families of related RNAs.
Nucleic acid folding family identification
true
beta12orEarlier
1.20
Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.
Nucleic acid folding energy calculation
true
beta12orEarlier
beta12orEarlier
Retrieve existing annotation (or documentation), typically annotation on a database entity.
Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.
Annotation retrieval
true
beta12orEarlier
Predict the biological or biochemical role of a protein, or other aspects of a protein function.
Protein function analysis
Protein functional analysis
For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
Protein function prediction
beta12orEarlier
Compare the functional properties of two or more proteins.
Protein function comparison
beta12orEarlier
1.6
Submit a molecular sequence to a database.
Sequence submission
true
beta12orEarlier
Analyse a known network of gene regulation.
Gene regulatory network comparison
Gene regulatory network modelling
Regulatory network comparison
Regulatory network modelling
Gene regulatory network analysis
beta12orEarlier
WHATIF:UploadPDB
Parse, prepare or load a user-specified data file so that it is available for use.
Data loading
Loading
Parsing
beta12orEarlier
1.6
Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
Sequence retrieval
true
beta12orEarlier
1.6
WHATIF:DownloadPDB
WHATIF:EchoPDB
Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.
This includes direct retrieval methods but not those that perform calculations on the sequence or structure.
Structure retrieval
true
beta12orEarlier
WHATIF:GetSurfaceDots
Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.
A dot has three coordinates (x,y,z) and (typically) a color.
Surface rendering
beta12orEarlier
1.12
Calculate the solvent accessibility ('accessible surface') for each atom in a structure.
Waters are not considered.
Protein atom surface calculation (accessible)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure.
Waters are not considered.
Protein atom surface calculation (accessible molecular)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('accessible surface') for each residue in a structure.
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
Protein residue surface calculation (accessible)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
Protein residue surface calculation (vacuum accessible)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure.
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
Protein residue surface calculation (accessible molecular)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
Protein residue surface calculation (vacuum molecular)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole.
Protein surface calculation (accessible molecular)
true
beta12orEarlier
1.12
Calculate the solvent accessibility ('accessible surface') for a structure as a whole.
Protein surface calculation (accessible)
true
beta12orEarlier
1.12
Calculate for each residue in a protein structure all its backbone torsion angles.
Backbone torsion angle calculation
true
beta12orEarlier
1.12
Calculate for each residue in a protein structure all its torsion angles.
Full torsion angle calculation
true
beta12orEarlier
1.12
Calculate for each cysteine (bridge) all its torsion angles.
Cysteine torsion angle calculation
true
beta12orEarlier
1.12
For each amino acid in a protein structure calculate the backbone angle tau.
Tau is the backbone angle N-Calpha-C (angle over the C-alpha).
Tau angle calculation
true
beta12orEarlier
WHATIF:ShowCysteineBridge
Detect cysteine bridges (from coordinate data) in a protein structure.
Cysteine bridge detection
beta12orEarlier
WHATIF:ShowCysteineFree
Detect free cysteines in a protein structure.
A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.
Free cysteine detection
beta12orEarlier
WHATIF:ShowCysteineMetal
Detect cysteines that are bound to metal in a protein structure.
Metal-bound cysteine detection
beta12orEarlier
1.12
Calculate protein residue contacts with nucleic acids in a structure.
Residue contact calculation (residue-nucleic acid)
true
beta12orEarlier
Calculate protein residue contacts with metal in a structure.
Residue-metal contact calculation
Protein-metal contact calculation
beta12orEarlier
1.12
Calculate ion contacts in a structure (all ions for all side chain atoms).
Residue contact calculation (residue-negative ion)
true
beta12orEarlier
WHATIF:ShowBumps
Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance.
Residue bump detection
beta12orEarlier
1.12
WHATIF:SymmetryContact
Calculate the number of symmetry contacts made by residues in a protein structure.
A symmetry contact is a contact between two atoms in different asymmetric unit.
Residue symmetry contact calculation
true
beta12orEarlier
1.12
Calculate contacts between residues and ligands in a protein structure.
Residue contact calculation (residue-ligand)
true
beta12orEarlier
WHATIF:HasSaltBridge
WHATIF:HasSaltBridgePlus
WHATIF:ShowSaltBridges
WHATIF:ShowSaltBridgesH
Calculate (and possibly score) salt bridges in a protein structure.
Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.
Salt bridge calculation
beta12orEarlier
1.12
WHATIF:ShowLikelyRotamers
WHATIF:ShowLikelyRotamers100
WHATIF:ShowLikelyRotamers200
WHATIF:ShowLikelyRotamers300
WHATIF:ShowLikelyRotamers400
WHATIF:ShowLikelyRotamers500
WHATIF:ShowLikelyRotamers600
WHATIF:ShowLikelyRotamers700
WHATIF:ShowLikelyRotamers800
WHATIF:ShowLikelyRotamers900
Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.
Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
Rotamer likelihood prediction
true
beta12orEarlier
1.12
WHATIF:ProlineMutationValue
Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein.
Proline mutation value calculation
true
beta12orEarlier
WHATIF: PackingQuality
Identify poorly packed residues in protein structures.
Residue packing validation
beta12orEarlier
WHATIF: ImproperQualityMax
WHATIF: ImproperQualitySum
Validate protein geometry, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. An example is validation of a Ramachandran plot of a protein structure.
Ramachandran plot validation
Protein geometry validation
beta12orEarlier
beta12orEarlier
WHATIF: PDB_sequence
Extract a molecular sequence from a PDB file.
PDB file sequence retrieval
true
beta12orEarlier
1.12
Identify HET groups in PDB files.
A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
HET group detection
true
beta12orEarlier
beta12orEarlier
Determine for residue the DSSP determined secondary structure in three-state (HSC).
DSSP secondary structure assignment
true
beta12orEarlier
1.12
WHATIF: PDBasXML
Reformat (a file or other report of) tertiary structure data.
Structure formatting
true
beta12orEarlier
Assign cysteine bonding state and disulfide bond partners in protein structures.
Protein cysteine and disulfide bond assignment
beta12orEarlier
1.12
Identify poor quality amino acid positions in protein structures.
Residue validation
true
beta12orEarlier
1.6
WHATIF:MovedWaterPDB
Query a tertiary structure database and retrieve water molecules.
Structure retrieval (water)
true
beta12orEarlier
Identify or predict siRNA duplexes in RNA.
siRNA duplex prediction
beta12orEarlier
Refine an existing sequence alignment.
Sequence alignment refinement
beta12orEarlier
1.6
Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).
Listfile processing
true
beta12orEarlier
Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences.
Sequence file editing
beta12orEarlier
1.6
Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.
Sequence alignment file processing
true
beta12orEarlier
beta13
Process (read and / or write) physicochemical property data for small molecules.
Small molecule data processing
true
beta12orEarlier
beta13
Search and retrieve documentation on a bioinformatics ontology.
Data retrieval (ontology annotation)
true
beta12orEarlier
beta13
Query an ontology and retrieve concepts or relations.
Data retrieval (ontology concept)
true
beta12orEarlier
Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
Representative sequence identification
beta12orEarlier
1.6
Perform basic (non-analytical) operations on a file of molecular tertiary structural data.
Structure file processing
true
beta12orEarlier
beta13
Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.
This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
Data retrieval (sequence profile)
true
beta12orEarlier
Perform a statistical data operation of some type, e.g. calibration or validation.
Significance testing
Statistical analysis
Statistical test
Statistical testing
Expectation maximisation
Gibbs sampling
Hypothesis testing
Omnibus test
Statistical calculation
beta12orEarlier
Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.
3D-1D scoring matrix construction
A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.
3D-1D scoring matrix generation
beta12orEarlier
Visualise transmembrane proteins, typically the transmembrane regions within a sequence.
Transmembrane protein rendering
Transmembrane protein visualisation
beta12orEarlier
beta13
An operation performing purely illustrative (pedagogical) purposes.
Demonstration
true
beta12orEarlier
beta13
Query a biological pathways database and retrieve annotation on one or more pathways.
Data retrieval (pathway or network)
true
beta12orEarlier
beta13
Query a database and retrieve one or more data identifiers.
Data retrieval (identifier)
true
beta12orEarlier
Calculate a density plot (of base composition) for a nucleotide sequence.
Nucleic acid density plotting
beta12orEarlier
Analyse one or more known molecular sequences.
Sequence analysis (general)
Sequence analysis
beta12orEarlier
Analyse molecular sequence motifs.
Sequence motif processing
Sequence motif analysis
beta12orEarlier
1.6
Process (read and / or write) protein interaction data.
Protein interaction data processing
true
beta12orEarlier
Analyse protein structural data.
Structure analysis (protein)
Protein structure analysis
beta12orEarlier
beta12orEarlier
Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.
Annotation processing
true
beta12orEarlier
beta12orEarlier
Analyse features in molecular sequences.
Sequence feature analysis
true
beta12orEarlier
true
Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output.
File handling
File processing
Report handling
Utility operation
Processing
Data handling
beta12orEarlier
beta12orEarlier
Analyse gene expression and regulation data.
Gene expression analysis
true
beta12orEarlier
1.6
Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.
Structural profile processing
true
beta12orEarlier
1.6
Process (read and / or write) an index of (typically a file of) biological data.
Data index processing
true
beta12orEarlier
1.6
Process (read and / or write) some type of sequence profile.
Sequence profile processing
true
beta12orEarlier
1.22
Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.
Protein function analysis
true
beta12orEarlier
Analyse, simulate or predict protein folding, typically by processing sequence and / or structural data. For example, predict sites of nucleation or stabilisation key to protein folding.
Protein folding modelling
Protein folding simulation
Protein folding site prediction
Protein folding analysis
beta12orEarlier
Analyse protein secondary structure data.
Secondary structure analysis (protein)
Protein secondary structure analysis
beta12orEarlier
beta13
Process (read and / or write) data on the physicochemical property of a molecule.
Physicochemical property data processing
true
beta12orEarlier
Predict oligonucleotide primers or probes.
Primer and probe prediction
Primer and probe design
beta12orEarlier
1.12
Process (read and / or write) data of a specific type, for example applying analytical methods.
Operation (typed)
true
beta12orEarlier
Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.
Search
Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.
Database search
beta12orEarlier
Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords.
Data extraction
Retrieval
Data retrieval (metadata)
Metadata retrieval
Data retrieval
beta12orEarlier
true
Predict, recognise, detect or identify some properties of a biomolecule.
Detection
Prediction
Recognition
Prediction and recognition
beta12orEarlier
true
Compare two or more things to identify similarities.
Comparison
beta12orEarlier
true
Refine or optimise some data model.
Optimisation and refinement
beta12orEarlier
true
Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.
Mathematical modelling
Modelling and simulation
beta12orEarlier
beta12orEarlier
Perform basic operations on some data or a database.
Data handling
true
beta12orEarlier
true
Validate some data.
Quality control
Validation
beta12orEarlier
true
Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.
Cartography
Mapping
beta12orEarlier
true
Design a biological entity (typically a molecular sequence or structure) with specific properties.
Design
beta12orEarlier
beta12orEarlier
Process (read and / or write) microarray data.
Microarray data processing
true
beta12orEarlier
1.18
Process (read and / or write) a codon usage table.
Codon usage table processing
true
beta12orEarlier
beta13
Retrieve a codon usage table and / or associated annotation.
Data retrieval (codon usage table)
true
beta12orEarlier
1.6
Process (read and / or write) a gene expression profile.
Gene expression profile processing
true
beta12orEarlier
Analyse gene expression patterns to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.
Gene sets can be defined beforehand by biological function, chromosome locations and so on.
Gene set testing
Identify classes of genes or proteins that are over or under-represented in a large set of genes or proteins. For example analysis of a set of genes corresponding to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed.
Functional enrichment analysis
GSEA
Gene-set over-represenation analysis
Gene set analysis
GO-term enrichment
Gene Ontology concept enrichment
Gene Ontology term enrichment
"Gene set analysis" (often used interchangeably or in an overlapping sense with "gene-set enrichment analysis") refers to the functional analysis (term enrichment) of a differentially expressed set of genes, rather than all genes analysed.
The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value.
Gene-set enrichment analysis
beta12orEarlier
Predict a network of gene regulation.
Gene regulatory network prediction
beta12orEarlier
1.12
Generate, analyse or handle a biological pathway or network.
Pathway or network processing
true
beta12orEarlier
Process (read and / or write) RNA secondary structure data.
RNA secondary structure analysis
beta12orEarlier
beta13
Process (read and / or write) RNA tertiary structure data.
Structure processing (RNA)
true
beta12orEarlier
Predict RNA tertiary structure.
RNA structure prediction
beta12orEarlier
Predict DNA tertiary structure.
DNA structure prediction
beta12orEarlier
1.12
Generate, process or analyse phylogenetic tree or trees.
Phylogenetic tree processing
true
beta12orEarlier
1.6
Process (read and / or write) protein secondary structure data.
Protein secondary structure processing
true
beta12orEarlier
1.6
Process (read and / or write) a network of protein interactions.
Protein interaction network processing
true
beta12orEarlier
1.6
Process (read and / or write) one or more molecular sequences and associated annotation.
Sequence processing
true
beta12orEarlier
1.6
Process (read and / or write) a protein sequence and associated annotation.
Sequence processing (protein)
true
beta12orEarlier
1.6
Process (read and / or write) a nucleotide sequence and associated annotation.
Sequence processing (nucleic acid)
true
beta12orEarlier
Compare two or more molecular sequences.
Sequence comparison
beta12orEarlier
1.6
Process (read and / or write) a sequence cluster.
Sequence cluster processing
true
beta12orEarlier
1.6
Process (read and / or write) a sequence feature table.
Feature table processing
true
beta12orEarlier
Includes methods that predict whole gene structure using a combination of multiple methods to achieve better predictions.
Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc.
Gene calling
Gene finding
Whole gene prediction
Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
Gene prediction
beta12orEarlier
1.16
Classify G-protein coupled receptors (GPCRs) into families and subfamilies.
GPCR classification
true
beta12orEarlier
Not sustainable to have protein type-specific concepts.
1.19
Predict G-protein coupled receptor (GPCR) coupling selectivity.
GPCR coupling selectivity prediction
true
beta12orEarlier
1.6
Process (read and / or write) a protein tertiary structure.
Structure processing (protein)
true
beta12orEarlier
1.12
Calculate the solvent accessibility for each atom in a structure.
Waters are not considered.
Protein atom surface calculation
true
beta12orEarlier
1.12
Calculate the solvent accessibility for each residue in a structure.
Protein residue surface calculation
true
beta12orEarlier
1.12
Calculate the solvent accessibility of a structure as a whole.
Protein surface calculation
true
beta12orEarlier
1.6
Process (read and / or write) a molecular sequence alignment.
Sequence alignment processing
true
beta12orEarlier
Identify or predict protein-protein binding sites.
Protein-protein binding site detection
Protein-protein binding site prediction
beta12orEarlier
1.6
Process (read and / or write) a molecular tertiary structure.
Structure processing
true
beta12orEarlier
1.6
Annotate a DNA map of some type with terms from a controlled vocabulary.
Map annotation
true
beta12orEarlier
beta13
Retrieve information on a protein.
Data retrieval (protein annotation)
true
beta12orEarlier
beta13
Retrieve a phylogenetic tree from a data resource.
Data retrieval (phylogenetic tree)
true
beta12orEarlier
beta13
Retrieve information on a protein interaction.
Data retrieval (protein interaction annotation)
true
beta12orEarlier
beta13
Retrieve information on a protein family.
Data retrieval (protein family annotation)
true
beta12orEarlier
beta13
Retrieve information on an RNA family.
Data retrieval (RNA family annotation)
true
beta12orEarlier
beta13
Retrieve information on a specific gene.
Data retrieval (gene annotation)
true
beta12orEarlier
beta13
Retrieve information on a specific genotype or phenotype.
Data retrieval (genotype and phenotype annotation)
true
beta12orEarlier
Compare the architecture of two or more protein structures.
Protein architecture comparison
beta12orEarlier
Identify the architecture of a protein structure.
Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces.
Protein architecture recognition
beta12orEarlier
The simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
Molecular dynamics simulation
Protein dynamics
Molecular dynamics
beta12orEarlier
Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).
Sequence analysis (nucleic acid)
Nucleic acid sequence alignment analysis
Sequence alignment analysis (nucleic acid)
Nucleic acid sequence analysis
beta12orEarlier
Analyse a protein sequence (using methods that are only applicable to protein sequences).
Sequence analysis (protein)
Protein sequence alignment analysis
Sequence alignment analysis (protein)
Protein sequence analysis
beta12orEarlier
Analyse known molecular tertiary structures.
Structure analysis
beta12orEarlier
Analyse nucleic acid tertiary structural data.
Nucleic acid structure analysis
beta12orEarlier
1.6
Process (read and / or write) a molecular secondary structure.
Secondary structure processing
true
beta12orEarlier
Compare two or more molecular tertiary structures.
Structure comparison
beta12orEarlier
Render a helical wheel representation of protein secondary structure.
Helical wheel rendering
Helical wheel drawing
beta12orEarlier
Render a topology diagram of protein secondary structure.
Topology diagram rendering
Topology diagram drawing
beta12orEarlier
Compare protein tertiary structures.
Structure comparison (protein)
Methods might identify structural neighbors, find structural similarities or define a structural core.
Protein structure comparison
beta12orEarlier
Compare protein secondary structures.
Protein secondary structure
Secondary structure comparison (protein)
Protein secondary structure alignment
Protein secondary structure comparison
beta12orEarlier
Predict the subcellular localisation of a protein sequence.
Protein cellular localization prediction
Protein subcellular localisation prediction
Protein targeting prediction
The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.
Subcellular localisation prediction
beta12orEarlier
1.12
Calculate contacts between residues in a protein structure.
Residue contact calculation (residue-residue)
true
beta12orEarlier
1.12
Identify potential hydrogen bonds between amino acid residues.
Hydrogen bond calculation (inter-residue)
true
beta12orEarlier
Predict the interactions of proteins with other proteins.
Protein-protein interaction detection
Protein-protein binding prediction
Protein-protein interaction prediction
Protein interaction prediction
beta12orEarlier
beta13
Process (read and / or write) codon usage data.
Codon usage data processing
true
beta12orEarlier
Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function.
Process (read and/or write) expression data from experiments measuring molecules (e.g. omics data), including analysis of one or more expression profiles, typically to interpret them in functional terms.
Expression data analysis
Gene expression analysis
Gene expression data analysis
Gene expression regulation analysis
Metagenomic inference
Microarray data analysis
Protein expression analysis
Expression analysis
beta12orEarlier
1.6
Process (read and / or write) a network of gene regulation.
Gene regulatory network processing
true
beta12orEarlier
Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
1.24
Generate, process or analyse a biological pathway or network.
Pathway or network analysis
true
beta12orEarlier
beta12orEarlier
Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.
Sequencing-based expression profile data analysis
true
beta12orEarlier
Predict, analyse, characterize or model splice sites, splicing events and so on, typically by comparing multiple nucleic acid sequences.
Splicing model analysis
Splicing analysis
beta12orEarlier
beta12orEarlier
Analyse raw microarray data.
Microarray raw data analysis
true
beta12orEarlier
1.19
Process (read and / or write) nucleic acid sequence or structural data.
Nucleic acid analysis
true
beta12orEarlier
1.19
Process (read and / or write) protein sequence or structural data.
Protein analysis
true
beta12orEarlier
beta13
Process (read and / or write) molecular sequence data.
Sequence data processing
true
beta12orEarlier
beta13
Process (read and / or write) molecular structural data.
Structural data processing
true
beta12orEarlier
1.6
Process (read and / or write) text.
Text processing
true
beta12orEarlier
1.18
Analyse a protein sequence alignment, typically to detect features or make predictions.
Protein sequence alignment analysis
true
beta12orEarlier
1.18
Analyse a protein sequence alignment, typically to detect features or make predictions.
Nucleic acid sequence alignment analysis
true
beta12orEarlier
1.18
Compare two or more nucleic acid sequences.
Nucleic acid sequence comparison
true
beta12orEarlier
1.18
Compare two or more protein sequences.
Protein sequence comparison
true
beta12orEarlier
Back-translate a protein sequence into DNA.
DNA back-translation
beta12orEarlier
1.8
Edit or change a nucleic acid sequence, either randomly or specifically.
Sequence editing (nucleic acid)
true
beta12orEarlier
1.8
Edit or change a protein sequence, either randomly or specifically.
Sequence editing (protein)
true
beta12orEarlier
1.22
Generate a nucleic acid sequence by some means.
Sequence generation (nucleic acid)
true
beta12orEarlier
1.22
Generate a protein sequence by some means.
Sequence generation (protein)
true
beta12orEarlier
1.8
Visualise, format or render a nucleic acid sequence.
Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
Nucleic acid sequence visualisation
true
beta12orEarlier
1.8
Visualise, format or render a protein sequence.
Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
Protein sequence visualisation
true
beta12orEarlier
Compare nucleic acid tertiary structures.
Structure comparison (nucleic acid)
Nucleic acid structure comparison
beta12orEarlier
1.6
Process (read and / or write) nucleic acid tertiary structure data.
Structure processing (nucleic acid)
true
beta12orEarlier
Generate a map of a DNA sequence annotated with positional or non-positional features of some type.
DNA mapping
beta12orEarlier
1.6
Process (read and / or write) a DNA map of some type.
Map data processing
true
beta12orEarlier
Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).
Protein hydropathy calculation
beta12orEarlier
Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.
Protein binding site detection
Protein binding site prediction
Binding site prediction
beta12orEarlier
Build clusters of similar structures, typically using scores from structural alignment methods.
Structural clustering
Structure clustering
beta12orEarlier
Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).
Sequence mapping
An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.
Sequence tagged site (STS) mapping
beta12orEarlier
true
Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.
Alignment construction
Alignment generation
Alignment
beta12orEarlier
Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification.
PMF
Peptide mass fingerprinting
Protein fingerprinting
Protein fragment weight comparison
beta12orEarlier
Compare the physicochemical properties of two or more proteins (or reference data).
Protein property comparison
beta12orEarlier
1.18
Compare two or more molecular secondary structures.
Secondary structure comparison
true
beta12orEarlier
1.12
Generate a Hopp and Woods plot of antigenicity of a protein.
Hopp and Woods plotting
true
beta12orEarlier
1.19
Generate a view of clustered quantitative data, annotated with textual information.
Cluster textual view generation
true
beta12orEarlier
In the case of microarray data, visualise clustered gene expression data as a set of profiles, where each profile shows the gene expression values of a cluster across samples on the X-axis.
Visualise clustered quantitative data as set of different profiles, where each profile is plotted versus different entities or samples on the X-axis.
Clustered quantitative data plotting
Clustered quantitative data rendering
Wave graph plotting
Microarray cluster temporal graph rendering
Microarray wave graph plotting
Microarray wave graph rendering
Clustering profile plotting
beta12orEarlier
1.19
Generate a dendrograph of raw, preprocessed or clustered expression (e.g. microarray) data.
Dendrograph plotting
true
beta12orEarlier
Generate a plot of distances (distance or correlation matrix) between expression values.
Distance map rendering
Distance matrix plotting
Distance matrix rendering
Proximity map rendering
Correlation matrix plotting
Correlation matrix rendering
Microarray distance map rendering
Microarray proximity map plotting
Microarray proximity map rendering
Proximity map plotting
beta12orEarlier
Visualise clustered expression data using a tree diagram.
Dendrogram plotting
Dendrograph plotting
Dendrograph visualisation
Expression data tree or dendrogram rendering
Expression data tree visualisation
Microarray 2-way dendrogram rendering
Microarray checks view rendering
Microarray matrix tree plot rendering
Microarray tree or dendrogram rendering
Dendrogram visualisation
beta12orEarlier
Examples for visualization are the distribution of variance over the components, loading and score plots.
Visualize the results of a principal component analysis (orthogonal data transformation). For example, visualization of the principal components (essential subspace) coming from a Principal Component Analysis (PCA) on the trajectory atomistic coordinates of a molecular structure.
PCA plotting
Principal component plotting
ED visualization
Essential Dynamics visualization
Microarray principal component plotting
Microarray principal component rendering
PCA visualization
Principal modes visualization
The use of Principal Component Analysis (PCA), a multivariate statistical analysis to obtain collective variables on the atomic positional fluctuations, helps to separate the configurational space in two subspaces: an essential subspace containing relevant motions, and another one containing irrelevant local fluctuations.
Principal component visualisation
beta12orEarlier
Comparison of two sets of quantitative data such as two samples of gene expression values.
Render a graph in which the values of two variables are plotted along two axes; the pattern of the points reveals any correlation.
Scatter chart plotting
Microarray scatter plot plotting
Microarray scatter plot rendering
Scatter plot plotting
beta12orEarlier
1.18
Visualise gene expression data where each band (or line graph) corresponds to a sample.
Whole microarray graph plotting
true
beta12orEarlier
Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.
Expression data tree-map rendering
Treemapping
Microarray tree-map rendering
Treemap visualisation
beta12orEarlier
In the case of micorarray data, visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.
Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles.
Box plot plotting
Microarray Box-Whisker plot plotting
Box-Whisker plot plotting
beta12orEarlier
Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.
Physical cartography
Physical mapping
beta12orEarlier
true
Apply analytical methods to existing data of a specific type.
This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling').
Analysis
beta12orEarlier
1.8
Process or analyse an alignment of molecular sequences or structures.
Alignment analysis
true
beta12orEarlier
1.16
Analyse a body of scientific text (typically a full text article from a scientific journal.)
Article analysis
true
beta12orEarlier
beta13
Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.
Molecular interaction analysis
true
beta12orEarlier
Includes analysis of raw experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
Analyse the interactions of proteins with other proteins.
Protein interaction analysis
Protein interaction raw data analysis
Protein interaction simulation
Protein-protein interaction analysis
beta12orEarlier
WHATIF: HETGroupNames
WHATIF:HasMetalContacts
WHATIF:HasMetalContactsPlus
WHATIF:HasNegativeIonContacts
WHATIF:HasNegativeIonContactsPlus
WHATIF:HasNucleicContacts
WHATIF:ShowDrugContacts
WHATIF:ShowDrugContactsShort
WHATIF:ShowLigandContacts
WHATIF:ShowProteiNucleicContacts
Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations.
HET group detection
Residue contact calculation (residue-ligand)
Residue contact calculation (residue-metal)
Residue contact calculation (residue-negative ion)
Residue contact calculation (residue-nucleic acid)
WHATIF:SymmetryContact
This includes identifying HET groups, which usually correspond to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit.
Residue distance calculation
beta12orEarlier
1.6
Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.
Alignment processing
true
beta12orEarlier
1.6
Process (read and / or write) a molecular tertiary (3D) structure alignment.
Structure alignment processing
true
beta12orEarlier
Calculate codon usage bias, e.g. generate a codon usage bias plot.
Codon usage bias plotting
Codon usage bias calculation
beta12orEarlier
1.22
Generate a codon usage bias plot.
Codon usage bias plotting
true
beta12orEarlier
Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc.
Codon usage fraction calculation
beta12orEarlier
true
Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.
Classification
beta12orEarlier
beta13
Process (read and / or write) molecular interaction data.
Molecular interaction data processing
true
beta12orEarlier
Assign molecular sequence(s) to a group or category.
Sequence classification
beta12orEarlier
Assign molecular structure(s) to a group or category.
Structure classification
beta12orEarlier
Compare two or more proteins (or some aspect) to identify similarities.
Protein comparison
beta12orEarlier
Compare two or more nucleic acids to identify similarities.
Nucleic acid comparison
beta12orEarlier
1.19
Predict, recognise, detect or identify some properties of proteins.
Prediction and recognition (protein)
true
beta12orEarlier
1.19
Predict, recognise, detect or identify some properties of nucleic acids.
Prediction and recognition (nucleic acid)
true
beta13
Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically.
Structure editing
beta13
Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.
Sequence alignment editing
beta13
Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
1.24
Render (visualise) a biological pathway or network.
Pathway or network visualisation
true
beta13
1.6
Predict general (non-positional) functional properties of a protein from analysing its sequence.
For functional properties that are positional, use 'Protein site detection' instead.
Protein function prediction (from sequence)
true
beta13
(jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed (consolidate with "Protein feature detection").
1.17
Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.
Protein sequence feature detection
true
beta13
1.18
Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.
Protein property calculation (from sequence)
true
beta13
1.6
Predict, recognise and identify positional features in proteins from analysing protein structure.
Protein feature prediction (from structure)
true
beta13
Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.
Protein feature prediction
Protein feature recognition
Protein secondary database search
Protein site detection
Protein site prediction
Protein site recognition
Sequence feature detection (protein)
Sequence profile database search
Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group.
Protein feature detection
beta13
1.6
Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.
Database search (by sequence)
true
beta13
Predict a network of protein interactions.
Protein interaction network prediction
beta13
Design (or predict) nucleic acid sequences with specific chemical or physical properties.
Gene design
Nucleic acid design
beta13
Edit a data entity, either randomly or specifically.
Editing
1.1
Evaluate a DNA sequence assembly, typically for purposes of quality control.
Assembly QC
Assembly quality evaluation
Sequence assembly QC
Sequence assembly quality evaluation
Sequence assembly validation
1.1
Align two or more (tpyically huge) molecular sequences that represent genomes.
Genome alignment construction
Whole genome alignment
Genome alignment
1.1
Reconstruction of a sequence assembly in a localised area.
Localised reassembly
1.1
Render and visualise a DNA sequence assembly.
Assembly rendering
Assembly visualisation
Sequence assembly rendering
Sequence assembly visualisation
1.1
Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer.
Base calling
Phred base calling
Phred base-calling
Base-calling
1.1
The mapping of methylation sites in a DNA (genome) sequence. Typically, the mapping of high-throughput bisulfite reads to the reference genome.
Bisulfite read mapping
Bisulfite sequence alignment
Bisulfite sequence mapping
Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.
Bisulfite mapping
1.1
Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.
Sequence contamination filtering
1.1
1.12
Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.
For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
Trim ends
true
1.1
1.12
Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
Trim vector
true
1.1
1.12
Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.
Trim to reference
true
1.1
Cut (remove) the end from a molecular sequence.
Trimming
Barcode sequence removal
Trim ends
Trim to reference
Trim vector
This includes
ennd trimming
Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.
For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
trimming to a reference sequence,
Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.
vector trimming
Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
Sequence trimming
1.1
Compare the features of two genome sequences.
Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.
Genome feature comparison
1.1
Detect errors in DNA sequences generated from sequencing projects).
Short read error correction
Short-read error correction
Sequencing error detection
1.1
Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.
Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.
Genotyping
1.1
Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
Genetic variation annotation
Sequence variation analysis
Variant analysis
Transcript variant analysis
Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
Genetic variation analysis
1.1
Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
Oligonucleotide alignment
Oligonucleotide alignment construction
Oligonucleotide alignment generation
Oligonucleotide mapping
Read alignment
Short oligonucleotide alignment
Short read alignment
Short read mapping
Short sequence read mapping
The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.
Read mapping
1.1
A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.
Split-read mapping
Split read mapping
1.1
Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.
Community profiling
Sample barcoding
DNA barcoding
1.1
1.19
Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.
SNP calling
true
1.1
"Polymorphism detection" and "Variant calling" are essentially the same thing - keeping the later as a more prevalent term nowadays.
1.24
Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.
Polymorphism detection
true
1.1
Visualise, format or render an image of a Chromatogram.
Chromatogram viewing
Chromatogram visualisation
1.1
Analyse cytosine methylation states in nucleic acid sequences.
Methylation profile analysis
Methylation analysis
1.1
1.19
Determine cytosine methylation status of specific positions in a nucleic acid sequences.
Methylation calling
true
1.1
Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay.
Genome methylation analysis
Global methylation analysis
Methylation level analysis (global)
Whole genome methylation analysis
1.1
Analysing the DNA methylation of specific genes or regions of interest.
Gene-specific methylation analysis
Methylation level analysis (gene-specific)
Gene methylation analysis
1.1
Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.
Genome browser
Genome browsing
Genome rendering
Genome viewing
Genome visualisation
1.1
Compare the sequence or features of two or more genomes, for example, to find matching regions.
Genomic region matching
Genome comparison
1.1
Generate an index of a genome sequence.
Burrows-Wheeler
Genome indexing (Burrows-Wheeler)
Genome indexing (suffix arrays)
Suffix arrays
Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome.
Genome indexing
1.1
1.12
Generate an index of a genome sequence using the Burrows-Wheeler algorithm.
The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.
Genome indexing (Burrows-Wheeler)
true
1.1
1.12
Generate an index of a genome sequence using a suffix arrays algorithm.
A suffix array consists of the lexicographically sorted list of suffixes of a genome.
Genome indexing (suffix arrays)
true
1.1
Analyse one or more spectra from mass spectrometry (or other) experiments.
Mass spectrum analysis
Spectrum analysis
Spectral analysis
1.1
Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment.
Peak assignment
Peak finding
Peak detection
1.1
Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps.
Scaffold construction
Scaffold generation
Scaffold may be positioned along a chromosome physical map to create a "golden path".
Scaffolding
1.1
Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.
Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.
Scaffold gap completion
1.1
Raw sequence data quality control.
Sequencing QC
Sequencing quality assessment
Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems.
Sequencing quality control
1.1
Pre-process sequence reads to ensure (or improve) quality and reliability.
Sequence read pre-processing
For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.
Read pre-processing
1.1
Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples.
Species frequency estimation
1.1
Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.
Protein binding peak detection
Peak-pair calling
Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo.
Peak calling
1.1
Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.
Differential expression analysis
Differential gene analysis
Differential gene expression analysis
Differentially expressed gene identification
Differential gene expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.
Differential gene expression profiling
1.1
1.21
Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.
Gene set testing
true
1.1
Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.
Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)
Variant classification
1.1
Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.
Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.
Variant prioritisation
1.1
Detect, identify and map mutations, such as single nucleotide polymorphisms, short indels and structural variants, in multiple DNA sequences. Typically the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware, to study genomic alterations.
Variant mapping
Allele calling
Exome variant detection
Genome variant detection
Germ line variant calling
Mutation detection
Somatic variant calling
de novo mutation detection
Methods often utilise a database of aligned reads.
Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant.
Variant detection
Variant calling
1.1
Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).
Structural variation discovery
Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.
Structural variation detection
1.1
Analyse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.
Exome sequence analysis
Exome assembly
1.1
Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.
Read depth analysis
1.1
Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes.
Gene expression QTL profiling
Gene expression quantitative trait loci profiling
eQTL profiling
Gene expression QTL analysis
1.1
Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.
Transcript copy number estimation
Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).
Copy number estimation
1.2
Adapter removal
Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).
Primer removal
1.2
Infer a transcriptome sequence by analysis of short sequence reads.
Transcriptome assembly
1.2
1.6
Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.
de novo transcriptome assembly
Transcriptome assembly (de novo)
true
1.2
1.6
Infer a transcriptome sequence by mapping short reads to a reference genome.
Transcriptome assembly (mapping)
true
1.3
Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc.
Sequence coordinate conversion
1.3
Calculate similarity between 2 or more documents.
Document similarity calculation
1.3
Cluster (group) documents on the basis of their calculated similarity.
Document clustering
1.3
Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents.
Concept mining
Entity chunking
Entity extraction
Entity identification
Event extraction
NER
Named-entity recognition
Named-entity and concept recognition
1.3
Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.
Accession mapping
Identifier mapping
The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence.
ID mapping
1.3
Process data in such a way that makes it hard to trace to the person which the data concerns.
Data anonymisation
Anonymisation
1.3
(jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved.
1.17
Search for and retrieve a data identifier of some kind, e.g. a database entry accession.
ID retrieval
true
1.4
Generate a checksum of a molecular sequence.
Sequence checksum generation
1.4
Construct a bibliography from the scientific literature.
Bibliography construction
Bibliography generation
1.4
Predict the structure of a multi-subunit protein and particularly how the subunits fit together.
Protein quaternary structure prediction
1.4
Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc.
Molecular surface analysis
1.4
Compare two or more ontologies, e.g. identify differences.
Ontology comparison
1.4
1.9
Compare two or more ontologies, e.g. identify differences.
Ontology comparison
true
1.4
Recognition of which format the given data is in.
Format identification
Format inference
Format recognition
'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology.
Format detection
The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs.
1.4
Split a file containing multiple data items into many files, each containing one item
File splitting
Splitting
1.6
true
Construct some data entity.
Construction
For non-analytical operations, see the 'Processing' branch.
Generation
1.6
(jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed.
1.17
Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions.
Nucleic acid sequence feature detection
true
1.6
Deposit some data in a database or some other type of repository or software system.
Data deposition
Data submission
Database deposition
Database submission
Submission
For non-analytical operations, see the 'Processing' branch.
Deposition
1.6
true
Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters).
Clustering
1.6
1.19
Construct some entity (typically a molecule sequence) from component pieces.
Assembly
true
1.6
true
Convert a data set from one form to another.
Conversion
1.6
Standardize or normalize data by some statistical method.
Normalisation
Standardisation
In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean.
Standardisation and normalisation
1.6
Combine multiple files or data items into a single file or object.
Aggregation
1.6
Compare two or more scientific articles.
Article comparison
1.6
true
Mathematical determination of the value of something, typically a properly of a molecule.
Calculation
1.6
Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
1.24
Predict a molecular pathway or network.
Pathway or network prediction
true
1.6
1.12
The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated.
Genome assembly
true
1.6
1.19
Generate a graph, or other visual representation, of data, showing the relationship between two or more variables.
Plotting
true
1.7
Image processing
The analysis of a image (typically a digital image) of some type in order to extract information from it.
Image analysis
1.7
Analysis of data from a diffraction experiment.
Diffraction data analysis
1.7
Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression.
Cell migration analysis
1.7
Processing of diffraction data into a corrected, ordered, and simplified form.
Diffraction data reduction
1.7
Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images.
Neurite measurement
1.7
The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment.
Diffraction profile fitting
Diffraction summation integration
Diffraction data integration
1.7
Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods.
Phasing
1.7
A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form.
The technique solves the phase problem, i.e. retrieve information concern phases of the structure.
Molecular replacement
1.7
A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms.
Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data.
Rigid body refinement
1.7
An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted.
Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM).
Single particle analysis
1.7
true
This is two related concepts.
Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle.
A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final 3D EM map.
Single particle alignment and classification
1.7
Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype.
Functional sequence clustering
Functional clustering
1.7
Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy.
Taxonomy assignment
Taxonomic profiling
Taxonomic classification
1.7
The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences.
Pathogenicity prediction
Virulence prediction
1.7
Analyse the correlation patterns among features/molecules across across a variety of experiments, samples etc.
Co-expression analysis
Gene co-expression network analysis
Gene expression correlation
Gene expression correlation analysis
Expression correlation analysis
1.7
true
Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data.
Correlation
1.7
Compute the covariance model for (a family of) RNA secondary structures.
RNA structure covariance model generation
1.7
1.18
Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds.
RNA secondary structure prediction (shape-based)
true
1.7
1.18
Prediction of nucleic-acid folding using sequence alignments as a source of data.
Nucleic acid folding prediction (alignment-based)
true
1.7
Count k-mers (substrings of length k) in DNA sequence data.
k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads.
k-mer counting
1.7
Reconstructing the inner node labels of a phylogenetic tree from its leafes.
Phylogenetic tree reconstruction
Gene tree reconstruction
Species tree reconstruction
Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one.
Phylogenetic reconstruction
1.7
Generate some data from a choosen probibalistic model, possibly to evaluate algorithms.
Probabilistic data generation
1.7
Generate sequences from some probabilistic model, e.g. a model that simulates evolution.
Probabilistic sequence generation
1.7
Identify or predict causes for antibiotic resistance from molecular sequence analysis.
Antimicrobial resistance prediction
1.8
Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed.
Enrichment
Over-representation analysis
Functional enrichment
Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data.
Enrichment analysis
1.8
Analyse a dataset with respect to concepts from an ontology of chemical structure, leveraging chemical similarity information.
Chemical class enrichment
Chemical similarity enrichment
1.8
Plot an incident curve such as a survival curve, death curve, mortality curve.
Incident curve plotting
1.8
Identify and map patterns of genomic variations.
Methods often utilise a database of aligned reads.
Variant pattern analysis
1.8
1.12
Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.
Mathematical modelling
true
1.9
Visualise images resulting from various types of microscopy.
Microscope image visualisation
1.9
Annotate an image of some sort, typically with terms from a controlled vocabulary.
Image annotation
1.9
Replace missing data with substituted values, usually by using some statistical or other mathematical approach.
Data imputation
Imputation
1.9
Visualise, format or render data from an ontology, typically a tree of terms.
Ontology browsing
Ontology visualisation
1.9
A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data.
Maximum occurence analysis
1.9
Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves.
Data model comparison
Schema comparison
Database comparison
1.9
1.24
Simulate the bevaviour of a biological pathway or network.
Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
Network simulation
true
1.9
Analyze read counts from RNA-seq experiments.
RNA-seq read count analysis
1.9
Identify and remove redudancy from a set of small molecule structures.
Chemical redundancy removal
1.9
Analyze time series data from an RNA-seq experiment.
RNA-seq time series data analysis
1.9
Simulate gene expression data, e.g. for purposes of benchmarking.
Simulated gene expression data generation
1.12
Identify semantic relations among entities and concepts within a text, using text mining techniques.
Relation discovery
Relation inference
Relationship discovery
Relationship extraction
Relationship inference
Relation extraction
1.12
Re-adjust the output of mass spectrometry experiments with shifted ppm values.
Mass spectra calibration
1.12
Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments.
Chromatographic alignment
1.12
The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point.
Deconvolution
Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution.
Deisotoping
1.12
Technique for determining the amount of proteins in a sample.
Protein quantitation
Protein quantification
1.12
Determination of peptide sequence from mass spectrum.
Peptide-spectrum-matching
Peptide identification
1.12
Calculate the isotope distribution of a given chemical species.
Isotopic distributions calculation
1.12
Prediction of retention time in a mass spectrometry experiment based on compositional and structural properties of the separated species.
Retention time calculation
Retention time prediction
1.12
Quantification without the use of chemical tags.
Label-free quantification
1.12
Quantification based on the use of chemical tags.
Labeled quantification
1.12
Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair).
MRM/SRM
1.12
Calculate number of identified MS2 spectra as approximation of peptide / protein quantity.
Spectral counting
1.12
Quantification analysis using stable isotope labeling by amino acids in cell culture.
SILAC
1.12
Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z.
iTRAQ
1.12
Quantification analysis using labeling based on 18O-enriched H2O.
18O labeling
1.12
Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow.
TMT-tag
1.12
Quantification analysis using chemical labeling by stable isotope dimethylation
Dimethyl
1.12
Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry.
Tag-based peptide identification
1.12
Analytical process that derives a peptide's amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database.
de Novo sequencing
1.12
Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum.
PTM identification
1.12
Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences.
Peptide database search
1.12
Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches.
Modification-tolerant peptide database search
Unrestricted peptide database search
Blind peptide database search
1.12
1.19
Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search.
Validation of peptide-spectrum matches
true
1.12
Validation of peptide-spectrum matches
Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search, and by comparison to search results with a database containing incorrect information.
Target-Decoy
1.12
Analyse data in order to deduce properties of an underlying distribution or population.
Empirical Bayes
Statistical inference
1.12
A statistical calculation to estimate the relationships among variables.
Regression
Regression analysis
1.12
Model a metabolic network. This can include 1) reconstruction to break down a metabolic pathways into reactions, enzymes, and other relevant information, and compilation of this into a mathematical model and 2) simulations of metabolism based on the model.
Metabolic network reconstruction
Metabolic network simulation
Metabolic pathway simulation
Metabolic reconstruction
The terms and synyonyms here reflect that for practical intents and purposes, "pathway" and "network" can be treated the same.
Metabolic network modelling
1.12
Predict the effect or function of an individual single nucleotide polymorphism (SNP).
SNP annotation
1.12
Prediction of genes or gene components from first principles, i.e. without reference to existing genes.
Gene prediction (ab-initio)
Ab-initio gene prediction
1.12
Prediction of genes or gene components by reference to homologous genes.
Empirical gene finding
Empirical gene prediction
Evidence-based gene prediction
Gene prediction (homology-based)
Similarity-based gene prediction
Homology prediction
Orthology prediction
Homology-based gene prediction
1.12
Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data.
Statistical modelling
1.12
Compare two or more molecular surfaces.
Molecular surface comparison
1.12
Annotate one or more sequences with functional information, such as cellular processes or metaobolic pathways, by reference to a controlled vocabulary - invariably the Gene Ontology (GO).
Sequence functional annotation
Gene functional annotation
1.12
Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info.
Variant filtering
1.12
Identify binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups.
Differential binding analysis
1.13
Analyze data from RNA-seq experiments.
RNA-Seq analysis
1.13
Visualise, format or render a mass spectrum.
Mass spectrum visualisation
1.13
Filter a set of files or data items according to some property.
Sequence filtering
rRNA filtering
Filtering
1.14
Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis.
Reference identification
1.14
Label-free quantification by integration of ion current (ion counting).
Ion current integration
Ion counting
1.14
Chemical tagging free amino groups of intact proteins with stable isotopes.
ICPL
Isotope-coded protein label
1.14
Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed.
C-13 metabolic labeling
N-15 metabolic labeling
This includes N-15 metabolic labeling (labeling all proteins and (possibly) all amino acids using N-15 enriched grown medium or feed) and C-13 metabolic labeling (labeling all proteins and (possibly) all amino acids using C-13 enriched grown medium or feed).
Metabolic labeling
1.15
Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis.
Sequence assembly (cross-assembly)
Cross-assembly
1.15
The comparison of samples from a metagenomics study, for example, by comparison of metagenome shotgun reads or assembled contig sequences, by comparison of functional profiles, or some other method.
Sample comparison
1.15
Differential protein analysis
The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup.
Differential protein expression analysis
Differential protein expression profiling
1.15
1.17
The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup.
Differential gene expression analysis
true
1.15
Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment.
Multiple sample visualisation
1.15
The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors.
Ancestral sequence reconstruction
Character mapping
Character optimisation
Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms.
Ancestral reconstruction
1.16
Site localisation of post-translational modifications in peptide or protein mass spectra.
PTM scoring
Site localisation
PTM localisation
1.16
Operations concerning the handling and use of other tools.
Endpoint management
Service management
1.16
An operation supporting the browsing or discovery of other tools and services.
Service discovery
1.16
An operation supporting the aggregation of other services (at least two) into a funtional unit, for the automation of some task.
Service composition
1.16
An operation supporting the calling (invocation) of other tools and services.
Service invocation
1.16
A data mining method typically used for studying biological networks based on pairwise correlations between variables.
WGCNA
Weighted gene co-expression network analysis
Weighted correlation network analysis
1.16
Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry.
Protein inference
Protein identification
1.16
Text annotation is the operation of adding notes, data and metadata, recognised entities and concepts, and their relations to a text (such as a scientific article).
Article annotation
Literature annotation
Text annotation
1.17
A method whereby data on several variants are "collapsed" into a single covariate based on regions such as genes.
Genome-wide association studies (GWAS) analyse a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. Traditional association techniques can lack the power to detect the significance of rare variants individually, or measure their compound effect (rare variant burden). "Collapsing methods" were developed to overcome these problems.
Collapsing methods
1.17
miRNA analysis
The analysis of microRNAs (miRNAs) : short, highly conserved small noncoding RNA molecules that are naturally occurring plant and animal genomes.
miRNA expression profiling
miRNA expression analysis
1.17
Counting and summarising the number of short sequence reads that map to genomic features.
Read summarisation
1.17
A technique whereby molecules with desired properties and function are isolated from libraries of random molecules, through iterative cycles of selection, amplification, and mutagenesis.
In vitro selection
1.17
The calculation of species richness for a number of individual samples, based on plots of the number of species as a function of the number of samples (rarefaction curves).
Species richness assessment
Rarefaction
1.17
An operation which groups reads or contigs and assigns them to operational taxonomic units.
Binning
Binning shotgun reads
Binning methods use one or a combination of compositional features or sequence similarity.
Read binning
1.17
true
Counting and measuring experimentally determined observations into quantities.
Quantitation
Quantification
1.17
Quantification of data arising from RNA-Seq high-throughput sequencing, typically the quantification of transcript abundances durnig transcriptome analysis in a gene expression study.
RNA-Seq quantitation
RNA-Seq quantification
1.17
Match experimentally measured mass spectrum to a spectrum in a spectral library or database.
Spectral library search
1.17
Sort a set of files or data items according to some property.
Sorting
1.17
Metabolite identification
Mass spectra identification of compounds that are produced by living systems. Including polyketides, terpenoids, phenylpropanoids, alkaloids and antibiotics.
De novo metabolite identification
Fragmenation tree generation
Metabolite identification
Natural product identification
1.19
Identify and assess specific genes or regulatory regions of interest that are differentially methylated.
Differentially-methylated region identification
DMR identification
1.21
Genotyping of multiple loci, typically characterizing microbial species isolates using internal fragments of multiple housekeeping genes.
MLST
Multilocus sequence typing
1.21
Calculate a theoretical mass spectrometry spectra for given sequences.
Spectrum prediction
Spectrum calculation
1.22
3D visualization of a molecular trajectory.
Trajectory visualization
1.22
Compute Essential Dynamics (ED) on a simulation trajectory: an analysis of molecule dynamics using PCA (Principal Component Analysis) applied to the atomic positional fluctuations.
ED
PCA
Principal modes
Principal Component Analysis (PCA) is a multivariate statistical analysis to obtain collective variables and reduce the dimensionality of the system.
Essential dynamics
1.22
Obtain force field parameters (charge, bonds, dihedrals, etc.) from a molecule, to be used in molecular simulations
Ligand parameterization
Molecule parameterization
Forcefield parameterisation
1.22
Analyse DNA sequences in order to determine an individual's DNA characteristics, for example in criminal forensics, parentage testing and so on.
DNA fingerprinting
DNA profiling
1.22
Predict or detect active sites in proteins; the region of an enzyme which binds a substrate bind and catalyses a reaction.
Active site detection
Active site prediction
1.22
Predict or detect ligand-binding sites in proteins; a region of a protein which reversibly binds a ligand for some biochemical purpose, such as transport or regulation of protein function.
Ligand-binding site detection
Peptide-protein binding prediction
Ligand-binding site prediction
1.22
Predict or detect metal ion-binding sites in proteins.
Metal-binding site detection
Protein metal-binding site prediction
Metal-binding site prediction
1.22
Model or simulate protein-protein binding using comparative modelling or other techniques.
Protein docking
Protein-protein docking
1.22
Predict DNA-binding proteins.
DNA-binding protein detection
DNA-protein interaction prediction
Protein-DNA interaction prediction
DNA-binding protein prediction
1.22
Predict RNA-binding proteins.
Protein-RNA interaction prediction
RNA-binding protein detection
RNA-protein interaction prediction
RNA-binding protein prediction
1.22
Predict or detect RNA-binding sites in protein sequences.
Protein-RNA binding site detection
Protein-RNA binding site prediction
RNA binding site detection
RNA binding site prediction
1.22
Predict or detect DNA-binding sites in protein sequences.
Protein-DNA binding site detection
Protein-DNA binding site prediction
DNA binding site detection
DNA binding site prediction
1.22
Identify or predict intrinsically disordered regions in proteins.
Protein disorder prediction
1.22
Extract structured information from unstructured ("free") or semi-structured textual documents.
IE
Information extraction
1.22
Retrieve resources from information systems matching a specific information need.
Information retrieval
1.24
Detects chimeric sequences (chimeras) from a sequence alignment.
Genome analysis
1.24
The determination of cytosine methylation status of specific positions in a nucleic acid sequences (usually reads from a bisulfite sequencing experiment).
Methylation calling
1.24
The identification of changes in DNA sequence or chromosome structure, usually in the context of diagnostic tests for disease, or to study ancestry or phylogeny.
Genetic testing
This can include indirect methods which reveal the results of genetic changes, such as RNA analysis to indicate gene expression, or biochemical analysis to identify expressed proteins.
DNA testing
1.24
The processing of reads from high-throughput sequencing machines.
Sequence read processing
1.24
Laboratory experiment to identify the differences between a specific genome (of an individual) and a reference genome (developed typically from many thousands of individuals).
WGS re-sequencing is used as golden standard to detect variations compared to a given reference genome, including small variants (SNP and InDels) as well as larger genome re-organisations (CNVs, translocations, etc.).
ows re-sequencing of complete genomes of any given organism with high resolution and high accuracy.
Resequencing
Whole_genome_sequencing
Amplicon panels
Amplicon sequencing
Amplicon-based sequencing
Highly targeted resequencing
WGR
WGRS
Whole genome resequencing
Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions.
Ultra-deep sequencing
Genome resequencing
1.24
Render (visualise) a network - typically a biological network of some sort.
Network rendering
Protein interaction network rendering
Protein interaction network visualisation
Network visualisation
1.24
Render (visualise) a biological pathway.
Pathway rendering
Pathway visualisation
1.24
Generate, process or analyse a biological network.
Biological network analysis
Biological network modelling
Biological network prediction
Network comparison
Network modelling
Network prediction
Network simulation
Network topology simulation
Network analysis
1.24
Generate, process or analyse a biological pathway.
Biological pathway analysis
Biological pathway modelling
Biological pathway prediction
Functional pathway analysis
Pathway comparison
Pathway modelling
Pathway prediction
Pathway simulation
Pathway analysis
1.24
Predict a metabolic pathway.
Metabolic pathway prediction
1.24
Interdisciplinary science focused on extracting information from chemical systems by data analytical approaches, for example multivariate statistics, applied mathematics, and computer science.
Chemometrics
Chemometrics
1.24
Assigning sequence reads to separate groups / files based on their index tag (sample origin).
Sequence demultiplexing
NGS sequence runs are often performed with multiple samples pooled together. In such cases, an index tag (or "barcode") - a unique sequence of between 6 and 12bp - is ligated to each sample's genetic material so that the sequence reads from different samples can be identified. The process of demultiplexing (dividing sequence reads into separate files for each index tag/sample) may be performed automatically by the sequencing hardware. Alternatively the reads may be lumped together in one file with barcodes still attached, requiring you to do the splitting using software. In such cases, a "mapping" file is used which indicates which barcodes correspond to which samples.
Demultiplexing
1.24
A process used in statistics, machine learning, and information theory that reduces the number of random variables by obtaining a set of principal variables.
Dimension reduction
Dimensionality reduction
1.24
A dimensionality reduction process that selects a subset of relevant features (variables, predictors) for use in model construction.
Attribute selection
Variable selection
Variable subset selection
Feature selection
1.24
A dimensionality reduction process which builds (ideally) informative and non-redundant values (features) from an initial set of measured data, to aid subsequent generalization, learning or interpretation.
Feature projection
Feature extraction
1.24
Virtual screening is used in drug discovery to identify potential drug compounds. It involves searching libraries of small molecules in order to identify those molecules which are most likely to bind to a drug target (typically a protein receptor or enzyme).
Ligand-based screening
Ligand-based virtual screening
Structure-based screening
Structured-based virtual screening
Virtual ligand screening
Virtual screening is widely used for lead identification, lead optimization, and scaffold hopping during drug design and discovery.
Virtual screening
1.24
Biotechnology approach that seeks to optimize cellular genetic and regulatory processes in order to increase the cells' production of a certain substance.
Metabolic engineering
1.24
The application of phylogenetic and other methods to estimate paleogeographical events such as speciation.
Biogeographic dating
Speciation dating
Species tree dating
Tree-dating
Tree dating
1.24
The development and use of mathematical models and systems analysis for the description of ecological processes, and applications such as the sustainable management of resources.
Ecological modelling
1.24
Mapping between gene tree nodes and species tree nodes or branches, to analyse and account for possible differences between gene histories and species histories, explaining this in terms of gene-scale events such as duplication, loss, transfer etc.
Gene tree / species tree reconciliation
Methods typically test for topological similarity between trees using for example a congruence index.
Phylogenetic tree reconciliation
1.24
The detection of genetic selection, or (the end result of) the process by which certain traits become more prevalent in a species than other traits.
Selection detection
1.25
A statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components.
Principal component analysis
1.25
Identify where sections of the genome are repeated and the number of repeats in the genome varies between individuals.
CNV detection
Copy number variation detection
1.25
Identify deletion events causing the number of repeats in the genome to vary between individuals.
Deletion detection
1.25
Identify duplication events causing the number of repeats in the genome to vary between individuals.
Duplication detection
1.25
Identify copy number variations which are complex, e.g. multi-allelic variations that have many structural alleles and have rearranged multiple times in the ancestral genomes.
Complex CNV detection
1.25
Identify amplification events causing the number of repeats in the genome to vary between individuals.
Amplification detection
1.25
Predict adhesins in protein sequences.
An adhesin is a cell-surface component that facilitate the adherence of a microorganism to a cell or surface. They are important virulence factors during establishment of infection and thus are targetted during vaccine development approaches that seek to block adhesin function and prevent adherence to host cell.
Adhesin prediction
1.25
Design new protein molecules with specific structural or functional properties.
Protein redesign
Rational protein design
de novo protein design
Protein design
1.25
The design of small molecules with specific biological activity, such as inhibitors or modulators for proteins that are of therapeutic interest. This can involve the modification of individual atoms, the addition or removal of molecular fragments, and the use reaction-based design to explore tractable synthesis options for the small molecule.
Drug design
Ligand-based drug design
Structure-based drug design
Structure-based small molecule design
Small molecule design can involve assessment of target druggability and flexibility, molecular docking, in silico fragment screening, molecular dynamics, and homology modeling.
There are two broad categories of small molecule design techniques when applied to the design of drugs: ligand-based drug design (e.g. ligand similarity) and structure-based drug design (ligand docking) methods. Ligand similarity methods exploit structural similarities to known active ligands, whereas ligand docking methods use the 3D structure of a target protein to predict the binding modes and affinities of ligands to it.
Small molecule design
beta12orEarlier
true
A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.
sumo:FieldOfStudy
Topic
http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research
http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method
http://purl.org/biotop/biotop.owl#Quality
http://www.ifomis.org/bfo/1.1/snap#Continuant
http://www.ifomis.org/bfo/1.1/snap#Quality
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality
http://www.onto-med.de/ontologies/gfo.owl#Category
http://www.onto-med.de/ontologies/gfo.owl#Perpetuant
beta12orEarlier
true
The processing and analysis of nucleic acid sequence, structural and other data.
Nucleic acid bioinformatics
Nucleic acid informatics
Nucleic_acids
Nucleic acid physicochemistry
Nucleic acid properties
Nucleic acids
http://purl.bioontology.org/ontology/MSH/D017422
http://purl.bioontology.org/ontology/MSH/D017423
beta12orEarlier
true
Archival, processing and analysis of protein data, typically molecular sequence and structural data.
Protein bioinformatics
Protein informatics
Proteins
Protein databases
Proteins
http://purl.bioontology.org/ontology/MSH/D020539
beta12orEarlier
1.13
The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.
Metabolites
true
beta12orEarlier
true
The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.
Sequences
Sequence_analysis
Biological sequences
Sequence databases
Sequence analysis
http://purl.bioontology.org/ontology/MSH/D017421
beta12orEarlier
true
The curation, processing, analysis and prediction of data about the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.
Biomolecular structure
Structural bioinformatics
Structure_analysis
Computational structural biology
Molecular structure
Structure data resources
Structure databases
Structures
This includes related concepts such as structural properties, alignments and structural motifs.
Structure analysis
http://purl.bioontology.org/ontology/MSH/D015394
beta12orEarlier
true
The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.
Structure_prediction
DNA structure prediction
Nucleic acid design
Nucleic acid folding
Nucleic acid structure prediction
Protein fold recognition
Protein structure prediction
RNA structure prediction
This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
Structure prediction
beta12orEarlier
beta12orEarlier
The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).
Alignment
true
beta12orEarlier
true
The study of evolutionary relationships amongst organisms.
Phylogeny
Phylogenetic clocks
Phylogenetic dating
Phylogenetic simulation
Phylogenetic stratigraphy
Phylogeny reconstruction
This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.
Phylogeny
http://purl.bioontology.org/ontology/MSH/D010802
beta12orEarlier
true
The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.
Functional_genomics
Functional genomics
beta12orEarlier
true
The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.
Ontology_and_terminology
Applied ontology
Ontologies
Ontology
Ontology relations
Terminology
Upper ontology
Ontology and terminology
http://purl.bioontology.org/ontology/MSH/D002965
beta12orEarlier
1.13
The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information.
Information retrieval
true
beta12orEarlier
true
VT 1.5.6 Bioinformatics
The archival, curation, processing and analysis of complex biological data.
Bioinformatics
This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation.
Bioinformatics
http://purl.bioontology.org/ontology/MSH/D016247
beta12orEarlier
true
Computer graphics
VT 1.2.5 Computer graphics
Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data.
Data rendering
Data_visualisation
Data visualisation
beta12orEarlier
1.3
The study of the thermodynamic properties of a nucleic acid.
Nucleic acid thermodynamics
true
beta12orEarlier
The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.
Nucleic acid structure
Nucleic_acid_structure_analysis
DNA melting
DNA structure
Nucleic acid denaturation
Nucleic acid thermodynamics
RNA alignment
RNA structure
RNA structure alignment
Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.
Nucleic acid structure analysis
beta12orEarlier
RNA sequences and structures.
RNA
Small RNA
RNA
beta12orEarlier
1.3
Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.
Nucleic acid restriction
true
beta12orEarlier
true
The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads).
Mapping
Genetic linkage
Linkage
Linkage mapping
Synteny
This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.
Mapping
beta12orEarlier
1.3
The study of codon usage in nucleotide sequence(s), genetic codes and so on.
Genetic codes and codon usage
true
beta12orEarlier
The translation of mRNA into protein and subsequent protein processing in the cell.
Protein_expression
Translation
Protein expression
beta12orEarlier
1.3
Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.
This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
Gene finding
true
beta12orEarlier
1.3
The transcription of DNA into mRNA.
Transcription
true
beta12orEarlier
beta13
Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).
Promoters
true
beta12orEarlier
beta12orEarlier
The folding (in 3D space) of nucleic acid molecules.
Nucleic acid folding
true
beta12orEarlier
true
Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.
Gene features
Gene_structure
Fusion genes
This includes the study of promoters, coding regions etc.
This incudes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information.
Gene structure
beta12orEarlier
true
Protein and peptide identification, especially in the study of whole proteomes of organisms.
Proteomics
Bottom-up proteomics
Discovery proteomics
MS-based targeted proteomics
MS-based untargeted proteomics
Metaproteomics
Peptide identification
Protein and peptide identification
Quantitative proteomics
Targeted proteomics
Top-down proteomics
Includes metaproteomics: proteomics analysis of an environmental sample.
Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein production data, for example in different cells or tissues.
Proteomics
http://purl.bioontology.org/ontology/MSH/D040901
beta12orEarlier
true
The elucidation of the three dimensional structure for all (available) proteins in a given organism.
Structural_genomics
Structural genomics
beta12orEarlier
true
The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.
Protein physicochemistry
Protein_properties
Protein hydropathy
Protein properties
beta12orEarlier
true
Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.
Protein_interactions
Protein interaction map
Protein interaction networks
Protein interactome
Protein-DNA interaction
Protein-DNA interactions
Protein-RNA interaction
Protein-RNA interactions
Protein-ligand interactions
Protein-nucleic acid interactions
Protein-protein interactions
This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.
Protein interactions
beta12orEarlier
true
Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
Protein_folding_stability_and_design
Protein design
Protein folding
Protein residue interactions
Protein stability
Rational protein design
Protein folding, stability and design
beta12orEarlier
beta13
Two-dimensional gel electrophoresis image and related data.
Two-dimensional gel electrophoresis
true
beta12orEarlier
1.13
An analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase.
Mass spectrometry
true
beta12orEarlier
beta13
Protein microarray data.
Protein microarrays
true
beta12orEarlier
1.3
The study of the hydrophobic, hydrophilic and charge properties of a protein.
Protein hydropathy
true
beta12orEarlier
The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export.
Protein_targeting_and_localisation
Protein localisation
Protein sorting
Protein targeting
Protein targeting and localisation
beta12orEarlier
1.3
Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.
Protein cleavage sites and proteolysis
true
beta12orEarlier
beta12orEarlier
The comparison of two or more protein structures.
Use this concept for methods that are exclusively for protein structure.
Protein structure comparison
true
beta12orEarlier
1.3
The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.
Protein residue interactions
true
beta12orEarlier
1.3
Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.
Protein-protein interactions
true
beta12orEarlier
1.3
Protein-ligand (small molecule) interactions.
Protein-ligand interactions
true
beta12orEarlier
1.3
Protein-DNA/RNA interactions.
Protein-nucleic acid interactions
true
beta12orEarlier
1.3
The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
Protein design
true
beta12orEarlier
beta12orEarlier
G-protein coupled receptors (GPCRs).
G protein-coupled receptors (GPCR)
true
beta12orEarlier
true
Carbohydrates, typically including structural information.
Carbohydrates
Carbohydrates
beta12orEarlier
true
Lipids and their structures.
Lipidomics
Lipids
Lipids
beta12orEarlier
true
Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.
Small_molecules
Amino acids
Chemical structures
Drug structures
Drug targets
Drugs and target structures
Metabolite structures
Peptides
Peptides and amino acids
Target structures
Targets
Toxins
Toxins and targets
CHEBI:23367
Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included.
This concept excludes macromolecules such as proteins and nucleic acids.
This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances.
Small molecules
beta12orEarlier
beta12orEarlier
Edit, convert or otherwise change a molecular sequence, either randomly or specifically.
Sequence editing
true
beta12orEarlier
true
The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.
Sequence_composition_complexity_and_repeats
Low complexity sequences
Nucleic acid repeats
Protein repeats
Protein sequence repeats
Repeat sequences
Sequence complexity
Sequence composition
Sequence repeats
This includes repetitive elements within a nucleic acid sequence, e.g. long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit.
This includes short repetitive subsequences (repeat sequences) in a protein sequence.
Sequence composition, complexity and repeats
beta12orEarlier
1.3
Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.
Motifs
Sequence motifs
true
beta12orEarlier
1.12
The comparison of two or more molecular sequences, for example sequence alignment and clustering.
The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.
Sequence comparison
true
beta12orEarlier
true
The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
Sequence_sites_features_and_motifs
Functional sites
HMMs
Sequence features
Sequence motifs
Sequence profiles
Sequence sites
Sequence sites, features and motifs
beta12orEarlier
beta12orEarlier
Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).
The query is a sequence-based entity such as another sequence, a motif or profile.
Sequence database search
true
beta12orEarlier
1.7
The comparison and grouping together of molecular sequences on the basis of their similarities.
This includes systems that generate, process and analyse sequence clusters.
Sequence clustering
true
beta12orEarlier
true
Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.
Protein 3D motifs
Protein_structural_motifs_and_surfaces
Protein structural features
Protein structural motifs
Protein surfaces
Structural motifs
This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc.
Protein structural motifs and surfaces
beta12orEarlier
1.3
The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment.
Structural (3D) profiles
true
beta12orEarlier
1.12
The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.
Protein structure prediction
true
beta12orEarlier
1.12
The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.
Nucleic acid structure prediction
true
beta12orEarlier
1.7
The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates.
Ab initio structure prediction
true
beta12orEarlier
1.4
The modelling of the three-dimensional structure of a protein using known sequence and structural data.
Homology modelling
true
beta12orEarlier
true
Molecular flexibility
Molecular motions
The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
Molecular_dynamics
Protein dynamics
This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc. This includes resources concerning flexibility and motion in protein and other molecular structures.
Molecular dynamics
beta12orEarlier
true
1.12
The modelling the structure of proteins in complex with small molecules or other macromolecules.
Molecular docking
true
beta12orEarlier
1.3
The prediction of secondary or supersecondary structure of protein sequences.
Protein secondary structure prediction
true
beta12orEarlier
1.3
The prediction of tertiary structure of protein sequences.
Protein tertiary structure prediction
true
beta12orEarlier
1.12
The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).
Protein fold recognition
true
beta12orEarlier
1.7
The alignment of molecular sequences or sequence profiles (representing sequence alignments).
This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.
Sequence alignment
true
beta12orEarlier
1.7
The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).
This includes the generation, storage, analysis, rendering etc. of structure alignments.
Structure alignment
true
beta12orEarlier
1.3
The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
Threading
true
beta12orEarlier
1.3
Sequence profiles; typically a positional, numerical matrix representing a sequence alignment.
Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
Sequence profiles and HMMs
true
beta12orEarlier
1.3
The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.
Currently too specific for the topic sub-ontology (but might be unobsoleted).
Phylogeny reconstruction
true
beta12orEarlier
true
The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.
Phylogenomics
Phylogenomics
beta12orEarlier
beta13
Simulated polymerase chain reaction (PCR).
Virtual PCR
true
beta12orEarlier
true
The assembly of fragments of a DNA sequence to reconstruct the original sequence.
Sequence_assembly
Assembly
Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'.
Sequence assembly
beta12orEarlier
true
Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.
DNA variation
Genetic_variation
Genomic variation
Mutation
Polymorphism
Somatic mutations
Genetic variation
http://purl.bioontology.org/ontology/MSH/D014644
beta12orEarlier
1.3
Microarrays, for example, to process microarray data or design probes and experiments.
Microarrays
http://purl.bioontology.org/ontology/MSH/D046228
true
beta12orEarlier
true
VT 3.1.7 Pharmacology and pharmacy
The study of drugs and their effects or responses in living systems.
Pharmacology
Computational pharmacology
Pharmacoinformatics
Pharmacology
beta12orEarlier
true
http://edamontology.org/topic_0197
The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.
Expression
Gene_expression
Codon usage
DNA chips
DNA microarrays
Gene expression profiling
Gene transcription
Gene translation
Transcription
Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.
This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.
Gene expression
http://purl.bioontology.org/ontology/MSH/D015870
beta12orEarlier
true
The regulation of gene expression.
Regulatory genomics
Gene regulation
beta12orEarlier
true
The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
Pharmacogenomics
Pharmacogenetics
Pharmacogenomics
beta12orEarlier
true
VT 3.1.4 Medicinal chemistry
The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.
Drug design
Medicinal_chemistry
This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
Medicinal chemistry
beta12orEarlier
1.3
Information on a specific fish genome including molecular sequences, genes and annotation.
Fish
true
beta12orEarlier
1.3
Information on a specific fly genome including molecular sequences, genes and annotation.
Flies
true
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
Information on a specific mouse or rat genome including molecular sequences, genes and annotation.
The resource may be specific to a group of mice / rats or all mice / rats.
Mice or rats
true
beta12orEarlier
1.3
Information on a specific worm genome including molecular sequences, genes and annotation.
Worms
true
beta12orEarlier
1.3
The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.
Literature analysis
true
beta12orEarlier
The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction.
NLP
Natural_language_processing
BioNLP
Literature mining
Text analytics
Text data mining
Text mining
Natural language processing
beta12orEarlier
Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary.
Data_submission_annotation_and_curation
Data curation
Data provenance
Database curation
Data submission, annotation and curation
beta12orEarlier
1.13
The management and manipulation of digital documents, including database records, files and reports.
Document, record and content management
true
beta12orEarlier
beta12orEarlier
Annotation of a molecular sequence.
Sequence annotation
true
beta12orEarlier
beta12orEarlier
Annotation of a genome.
Genome annotation
true
beta12orEarlier
Spectroscopy
An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.
NMR spectroscopy
Nuclear magnetic resonance spectroscopy
NMR
HOESY
Heteronuclear Overhauser Effect Spectroscopy
NOESY
Nuclear Overhauser Effect Spectroscopy
ROESY
Rotational Frame Nuclear Overhauser Effect Spectroscopy
NMR
beta12orEarlier
1.12
The classification of molecular sequences based on some measure of their similarity.
Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.
Sequence classification
true
beta12orEarlier
1.3
primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.
Protein classification
true
beta12orEarlier
beta12orEarlier
Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.
This includes comparison, discovery, recognition etc. of sequence motifs.
Sequence motif or profile
true
beta12orEarlier
true
Protein chemical modifications, e.g. post-translational modifications.
PTMs
Post-translational modifications
Protein post-translational modification
Protein_modifications
Post-translation modifications
Protein chemical modifications
Protein post-translational modifications
GO:0006464
MOD:00000
EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)
Protein modifications
beta12orEarlier
true
http://edamontology.org/topic_3076
Molecular interactions, biological pathways, networks and other models.
Molecular_interactions_pathways_and_networks
Biological models
Biological networks
Biological pathways
Cellular process pathways
Disease pathways
Environmental information processing pathways
Gene regulatory networks
Genetic information processing pathways
Interactions
Interactome
Metabolic pathways
Molecular interactions
Networks
Pathways
Signal transduction pathways
Signaling pathways
Molecular interactions, pathways and networks
beta12orEarlier
true
VT 1.3 Information sciences
VT 1.3.3 Information retrieval
VT 1.3.4 Information management
VT 1.3.5 Knowledge management
VT 1.3.99 Other
The study and practice of information processing and use of computer information systems.
Information management
Information science
Knowledge management
Informatics
Informatics
beta12orEarlier
1.3
Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.
Literature data resources
true
beta12orEarlier
true
Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.
Laboratory_Information_management
Laboratory resources
Laboratory information management
beta12orEarlier
1.3
General cell culture or data on a specific cell lines.
Cell and tissue culture
true
beta12orEarlier
true
VT 1.5.15 Ecology
The ecological and environmental sciences and especially the application of information technology (ecoinformatics).
Ecology
Computational ecology
Ecoinformatics
Ecological informatics
Ecosystem science
Ecology
http://purl.bioontology.org/ontology/MSH/D004777
beta12orEarlier
Electron diffraction experiment
The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light.
Electron_microscopy
Electron crystallography
SEM
Scanning electron microscopy
Single particle electron microscopy
TEM
Transmission electron microscopy
Electron microscopy
beta12orEarlier
beta13
The cell cycle including key genes and proteins.
Cell cycle
true
beta12orEarlier
1.13
The physicochemical, biochemical or structural properties of amino acids or peptides.
Peptides and amino acids
true
beta12orEarlier
1.3
A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).
Organelles
true
beta12orEarlier
1.3
Ribosomes, typically of ribosome-related genes and proteins.
Ribosomes
true
beta12orEarlier
beta13
A database about scents.
Scents
true
beta12orEarlier
1.13
The structures of drugs, drug target, their interactions and binding affinities.
Drugs and target structures
true
beta12orEarlier
true
A specific organism, or group of organisms, used to study a particular aspect of biology.
Organisms
Model_organisms
This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism.
Model organisms
beta12orEarlier
true
Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.
Genomics
Exomes
Genome annotation
Genomes
Personal genomics
Synthetic genomics
Viral genomics
Whole genomes
Genomics
http://purl.bioontology.org/ontology/MSH/D023281
beta12orEarlier
true
Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.
Genes, gene family or system
Gene_and protein_families
Gene families
Gene family
Gene system
Protein families
Protein sequence classification
A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.
Gene and protein families
beta12orEarlier
1.13
Study of chromosomes.
Chromosomes
true
beta12orEarlier
true
The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.
Genotype and phenotype resources
Genotype-phenotype
Genotype-phenotype analysis
Genotype_and_phenotype
Genotype
Genotyping
Phenotype
Phenotyping
Genotype and phenotype
beta12orEarlier
beta12orEarlier
Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.
Gene expression and microarray
true
beta12orEarlier
true
Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence.
Probes_and_primers
Primer quality
Primers
Probes
This includes the design of primers for PCR and DNA amplification or the design of molecular probes.
Probes and primers
http://purl.bioontology.org/ontology/MSH/D015335
beta12orEarlier
true
VT 3.1.6 Pathology
Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.
Disease
Pathology
Pathology
beta12orEarlier
1.3
A particular protein, protein family or other group of proteins.
Specific protein
Specific protein resources
true
beta12orEarlier
true
VT 1.5.25 Taxonomy
Organism classification, identification and naming.
Taxonomy
Taxonomy
beta12orEarlier
1.8
Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.
Protein sequence analysis
true
beta12orEarlier
1.8
The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.
Nucleic acid sequence analysis
true
beta12orEarlier
1.3
The repetitive nature of molecular sequences.
Repeat sequences
true
beta12orEarlier
1.3
The (character) complexity of molecular sequences, particularly regions of low complexity.
Low complexity sequences
true
beta12orEarlier
beta13
A specific proteome including protein sequences and annotation.
Proteome
true
beta12orEarlier
DNA sequences and structure, including processes such as methylation and replication.
DNA analysis
DNA
Ancient DNA
Chromosomes
The DNA sequences might be coding or non-coding sequences.
DNA
beta12orEarlier
1.13
Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames
Coding RNA
true
beta12orEarlier
true
Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).
Functional_regulatory_and_non-coding_RNA
Functional RNA
Long ncRNA
Long non-coding RNA
Non-coding RNA
Regulatory RNA
Small and long non-coding RNAs
Small interfering RNA
Small ncRNA
Small non-coding RNA
Small nuclear RNA
Small nucleolar RNA
lncRNA
miRNA
microRNA
ncRNA
piRNA
piwi-interacting RNA
siRNA
snRNA
snoRNA
Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).
Functional, regulatory and non-coding RNA
beta12orEarlier
1.3
One or more ribosomal RNA (rRNA) sequences.
rRNA
true
beta12orEarlier
1.3
One or more transfer RNA (tRNA) sequences.
tRNA
true
beta12orEarlier
1.8
Protein secondary structure or secondary structure alignments.
This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.
Protein secondary structure
true
beta12orEarlier
1.3
RNA secondary or tertiary structure and alignments.
RNA structure
true
beta12orEarlier
1.8
Protein tertiary structures.
Protein tertiary structure
true
beta12orEarlier
1.3
Classification of nucleic acid sequences and structures.
Nucleic acid classification
true
beta12orEarlier
1.14
Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.
Protein families
true
beta12orEarlier
true
Protein tertiary structural domains and folds in a protein or polypeptide chain.
Protein_folds_and_structural_domains
Intramembrane regions
Protein domains
Protein folds
Protein membrane regions
Protein structural domains
Protein topological domains
Protein transmembrane regions
Transmembrane regions
This includes topological domains such as cytoplasmic regions in a protein.
This includes trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. For example, the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.
Protein folds and structural domains
beta12orEarlier
1.3
Nucleotide sequence alignments.
Nucleic acid sequence alignment
true
beta12orEarlier
1.3
Protein sequence alignments.
A sequence profile typically represents a sequence alignment.
Protein sequence alignment
true
beta12orEarlier
1.3
The archival, detection, prediction and analysis ofpositional features such as functional sites in nucleotide sequences.
Nucleic acid sites and features
true
beta12orEarlier
1.3
The detection, identification and analysis of positional features in proteins, such as functional sites.
Protein sites and features
true
beta12orEarlier
Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.
Transcription_factors_and_regulatory_sites
-10 signals
-35 signals
Attenuators
CAAT signals
CAT box
CCAAT box
CpG islands
Enhancers
GC signals
Isochores
Promoters
TATA signals
TFBS
Terminators
Transcription factor binding sites
Transcription factors
Transcriptional regulatory sites
This includes CpG rich regions (isochores) in a nucleotide sequence.
This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators.
Transcription factors and regulatory sites
beta12orEarlier
1.0
Protein phosphorylation and phosphorylation sites in protein sequences.
Phosphorylation sites
true
beta12orEarlier
1.13
Metabolic pathways.
Metabolic pathways
true
beta12orEarlier
1.13
Signaling pathways.
Signaling pathways
true
beta12orEarlier
1.3
Protein and peptide identification
Protein and peptide identification
true
beta12orEarlier
Biological or biomedical analytical workflows or pipelines.
Pipelines
Workflows
Software integration
Tool integration
Tool interoperability
Workflows
beta12orEarlier
1.0
Structuring data into basic types and (computational) objects.
Data types and objects
true
beta12orEarlier
1.3
Theoretical biology
Theoretical biology
true
beta12orEarlier
1.3
Mitochondria, typically of mitochondrial genes and proteins.
Mitochondria
true
beta12orEarlier
Plant science
VT 1.5.10 Botany
VT 1.5.22 Plant science
Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.
Botany
Plant
Plant science
Plants
Plant_biology
Plant anatomy
Plant cell biology
Plant ecology
Plant genetics
Plant physiology
The resource may be specific to a plant, a group of plants or all plants.
Plant biology
beta12orEarlier
VT 1.5.28
Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.
Virology
Virology
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
VT 1.5.21 Mycology
Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.
Yeast
The resource may be specific to a fungus, a group of fungi or all fungi.
Fungi
true
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). Definition is wrong anyway.
1.17
Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
The resource may be specific to a pathogen, a group of pathogens or all pathogens.
Pathogens
true
beta12orEarlier
1.3
Arabidopsis-specific data.
Arabidopsis
true
beta12orEarlier
1.3
Rice-specific data.
Rice
true
beta12orEarlier
1.3
Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny.
Genetic mapping and linkage
true
beta12orEarlier
true
The study (typically comparison) of the sequence, structure or function of multiple genomes.
Comparative_genomics
Comparative genomics
beta12orEarlier
Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.
Mobile_genetic_elements
Transposons
Mobile genetic elements
beta12orEarlier
beta13
Human diseases, typically describing the genes, mutations and proteins implicated in disease.
Human disease
true
beta12orEarlier
true
VT 3.1.3 Immunology
The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.
Immunology
Immunology
http://purl.bioontology.org/ontology/MSH/D007120
http://purl.bioontology.org/ontology/MSH/D007125
beta12orEarlier
true
Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.
Membrane_and_lipoproteins
Lipoproteins
Membrane proteins
Transmembrane proteins
Membrane and lipoproteins
beta12orEarlier
true
Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.
Enzymology
Enzymes
Enzymes
beta12orEarlier
1.13
PCR primers and hybridisation oligos in a nucleic acid sequence.
Primers
true
beta12orEarlier
1.13
Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.
PolyA signal or sites
true
beta12orEarlier
1.13
CpG rich regions (isochores) in a nucleotide sequence.
CpG island and isochores
true
beta12orEarlier
1.13
Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.
Restriction sites
true
beta12orEarlier
1.13
Splice sites in a nucleotide sequence or alternative RNA splicing events.
Splice sites
true
beta12orEarlier
1.13
Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.
Matrix/scaffold attachment sites
true
beta12orEarlier
1.13
Operons (operators, promoters and genes) from a bacterial genome.
Operon
true
beta12orEarlier
1.13
Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.
Promoters
true
beta12orEarlier
true
VT 1.5.24 Structural biology
The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.
Structural_biology
Structural assignment
Structural determination
Structure determination
This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
Structural biology
beta12orEarlier
1.13
Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.
Protein membrane regions
true
beta12orEarlier
1.13
The comparison of two or more molecular structures, for example structure alignment and clustering.
This might involve comparison of secondary or tertiary (3D) structural information.
Structure comparison
true
beta12orEarlier
true
The study of gene and protein function including the prediction of functional properties of a protein.
Functional analysis
Function_analysis
Protein function analysis
Protein function prediction
Function analysis
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
Bacteriology
VT 1.5.2 Bacteriology
Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.
The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
Prokaryotes and Archaea
true
beta12orEarlier
1.3
Protein data resources.
Protein databases
true
beta12orEarlier
1.3
Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
Structure determination
true
beta12orEarlier
true
VT 1.5.11 Cell biology
Cells, such as key genes and proteins involved in the cell cycle.
Cell_biology
Cells
Cellular processes
Protein subcellular localization
Cell biology
beta12orEarlier
beta13
Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.
Classification
true
beta12orEarlier
1.3
Lipoproteins (protein-lipid assemblies).
Lipoproteins
true
beta12orEarlier
beta12orEarlier
Visualise a phylogeny, for example, render a phylogenetic tree.
Phylogeny visualisation
true
beta12orEarlier
true
The application of information technology to chemistry in biological research environment.
Chemical informatics
Chemoinformatics
Cheminformatics
Cheminformatics
beta12orEarlier
true
The holistic modelling and analysis of complex biological systems and the interactions therein.
Systems_biology
Biological modelling
Biological system modelling
Systems modelling
This includes databases of models and methods to construct or analyse a model.
Systems biology
http://purl.bioontology.org/ontology/MSH/D049490
beta12orEarlier
The application of statistical methods to biological problems.
Statistics_and_probability
Bayesian methods
Biostatistics
Descriptive statistics
Gaussian processes
Inferential statistics
Markov processes
Multivariate statistics
Probabilistic graphical model
Probability
Statistics
Statistics and probability
http://en.wikipedia.org/wiki/Biostatistics
http://purl.bioontology.org/ontology/MSH/D056808
beta12orEarlier
beta12orEarlier
Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).
The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
Structure database search
true
beta12orEarlier
true
The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking).
Molecular_modelling
Comparative modelling
Docking
Homology modeling
Homology modelling
Molecular docking
Molecular modelling
beta12orEarlier
1.2
The prediction of functional properties of a protein.
Protein function prediction
true
beta12orEarlier
1.13
Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.
SNP
true
beta12orEarlier
beta12orEarlier
Predict transmembrane domains and topology in protein sequences.
Transmembrane protein prediction
true
beta12orEarlier
beta12orEarlier
The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.
Use this concept for methods that are exclusively for nucleic acid structures.
Nucleic acid structure comparison
true
beta12orEarlier
1.13
Exons in a nucleotide sequences.
Exons
true
beta12orEarlier
1.13
Transcription of DNA into RNA including the regulation of transcription.
Gene transcription
true
beta12orEarlier
DNA mutation.
DNA_mutation
DNA mutation
beta12orEarlier
true
VT 3.2.16 Oncology
The study of cancer, for example, genes and proteins implicated in cancer.
Cancer biology
Oncology
Cancer
Neoplasm
Neoplasms
Oncology
beta12orEarlier
1.13
Structural and associated data for toxic chemical substances.
Toxins and targets
true
beta12orEarlier
1.13
Introns in a nucleotide sequences.
Introns
true
beta12orEarlier
beta12orEarlier
A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.
Tool topic
true
beta12orEarlier
beta12orEarlier
A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.
Study topic
true
beta12orEarlier
1.3
Biological nomenclature (naming), symbols and terminology.
Nomenclature
true
beta12orEarlier
1.3
The genes, gene variations and proteins involved in one or more specific diseases.
Disease genes and proteins
true
beta12orEarlier
true
http://edamontology.org/topic_3040
Protein secondary or tertiary structural data and/or associated annotation.
Protein structure
Protein_structure_analysis
Protein tertiary structure
Protein structure analysis
beta12orEarlier
The study of human beings in general, including the human genome and proteome.
Humans
Human_biology
Human biology
beta12orEarlier
1.3
Informatics resource (typically a database) primarily focussed on genes.
Gene resources
true
beta12orEarlier
1.3
Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.
Yeast
true
beta12orEarlier
(jison) Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.
The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
Eukaryotes
true
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.
The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
Invertebrates
true
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
Vertebrates
true
beta12orEarlier
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
1.17
Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.
The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
Unicellular eukaryotes
true
beta12orEarlier
1.3
Protein secondary or tertiary structure alignments.
Protein structure alignment
true
beta12orEarlier
The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample.
Crystallography
X-ray_diffraction
X-ray crystallography
X-ray microscopy
X-ray diffraction
beta12orEarlier
1.3
Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.
Ontologies, nomenclature and classification
http://purl.bioontology.org/ontology/MSH/D002965
true
beta12orEarlier
Immunity-related proteins and their ligands.
Immunoproteins_and_antigens
Antigens
Immunopeptides
Immunoproteins
Therapeutic antibodies
This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."
Immunoproteins and antigens
beta12orEarlier
beta12orEarlier
Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.
CHEBI:23367
Molecules
true
beta12orEarlier
true
VT 3.1.9 Toxicology
Toxins and the adverse effects of these chemical substances on living organisms.
Toxicology
Computational toxicology
Toxicoinformatics
Toxicology
beta12orEarlier
beta13
Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously.
Next-generation sequencing
High-throughput sequencing
true
beta12orEarlier
1.13
Gene regulatory networks.
Gene regulatory networks
true
beta12orEarlier
beta12orEarlier
Informatics resources dedicated to one or more specific diseases (not diseases in general).
Disease (specific)
true
beta12orEarlier
1.13
Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.
VNTR
true
beta12orEarlier
1.13
Microsatellite polymorphism in a DNA sequence.
Microsatellites
true
beta12orEarlier
1.13
Restriction fragment length polymorphisms (RFLP) in a DNA sequence.
RFLP
true
beta12orEarlier
true
DNA polymorphism.
DNA_polymorphism
Microsatellites
RFLP
SNP
Single nucleotide polymorphism
VNTR
Variable number of tandem repeat polymorphism
snps
Includes microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.
Includes restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.
Includes single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.
Includes variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.
DNA polymorphism
beta12orEarlier
1.3
Topic for the design of nucleic acid sequences with specific conformations.
Nucleic acid design
true
beta13
1.3
The design of primers for PCR and DNA amplification or the design of molecular probes.
Primer or probe design
true
beta13
1.2
Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.
Structure databases
true
beta13
1.2
Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.
Nucleic acid structure
true
beta13
1.3
Molecular sequence data resources, including sequence sites, alignments, motifs and profiles.
Sequence databases
true
beta13
1.3
Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
Nucleic acid sequences
true
beta13
1.3
Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
Protein sequences
true
beta13
1.3
Protein interaction networks
Protein interaction networks
true
beta13
true
VT 1.5.4 Biochemistry and molecular biology
The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.
Molecular_biology
Biological processes
Molecular biology
beta13
1.3
Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.
Mammals
true
beta13
true
VT 1.5.5 Biodiversity conservation
The degree of variation of life forms within a given ecosystem, biome or an entire planet.
Biodiversity
Biodiversity
http://purl.bioontology.org/ontology/MSH/D044822
beta13
1.3
The comparison, grouping together and classification of macromolecules on the basis of sequence similarity.
This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.
Sequence clusters and classification
true
beta13
true
The study of genes, genetic variation and heredity in living organisms.
Genetics
Genes
Heredity
Genetics
http://purl.bioontology.org/ontology/MSH/D005823
beta13
true
The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).
Quantitative_genetics
Quantitative genetics
beta13
true
The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow.
Population_genetics
Population genetics
beta13
1.3
Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).
Regulatory RNA
true
beta13
1.13
The documentation of resources such as tools, services and databases and how to get help.
Documentation and help
true
beta13
1.3
The structural and functional organisation of genes and other genetic elements.
Genetic organisation
true
beta13
true
The application of information technology to health, disease and biomedicine.
Biomedical informatics
Clinical informatics
Health and disease
Health informatics
Healthcare informatics
Medical_informatics
Medical informatics
beta13
true
VT 1.5.14 Developmental biology
How organisms grow and develop.
Developmental_biology
Development
Developmental biology
beta13
true
The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.
Embryology
Embryology
beta13
true
VT 3.1.1 Anatomy and morphology
The form and function of the structures of living organisms.
Anatomy
Anatomy
beta13
true
The scientific literature, language processing, reference information, and documentation.
Language
Literature
Literature_and_language
Bibliography
Citations
Documentation
References
Scientific literature
This includes the documentation of resources such as tools, services and databases, user support, how to get help etc.
Literature and language
http://purl.bioontology.org/ontology/MSH/D011642
beta13
true
Life science
Life sciences
VT 1.5 Biological sciences
VT 1.5.1 Aerobiology
VT 1.5.13 Cryobiology
VT 1.5.23 Reproductive biology
VT 1.5.3 Behavioural biology
VT 1.5.7 Biological rhythm
VT 1.5.8 Biology
VT 1.5.99 Other
The study of life and living organisms, including their morphology, biochemistry, physiology, development, evolution, and so on.
Biological science
Biology
Aerobiology
Behavioural biology
Biological rhythms
Chronobiology
Cryobiology
Reproductive biology
Biology
beta13
true
Databases
VT 1.3.1 Data management
The development and use of architectures, policies, practices and procedures for management of data.
Data management
Databases and information systems
Information systems
Biological_databases
Biological databases
http://purl.bioontology.org/ontology/MSH/D030541
beta13
1.3
The detection of the positional features, such as functional and other key sites, in molecular sequences.
Sequence feature detection
http://purl.bioontology.org/ontology/MSH/D058977
true
beta13
1.3
The detection of positional features such as functional sites in nucleotide sequences.
Nucleic acid feature detection
true
beta13
1.3
The detection, identification and analysis of positional protein sequence features, such as functional sites.
Protein feature detection
true
beta13
1.2
Topic for modelling biological systems in mathematical terms.
Biological system modelling
true
beta13
The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means.
Data collection
Data acquisition
beta13
1.3
Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.
Genes and proteins resources
true
beta13
1.13
Topological domains such as cytoplasmic regions in a protein.
Protein topological domains
true
beta13
true
Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
Protein_variants
Protein variants
beta13
1.12
Regions within a nucleic acid sequence containing a signal that alters a biological function.
Expression signals
true
beta13
Nucleic acids binding to some other molecule.
DNA_binding_sites
Matrix-attachment region
Matrix/scaffold attachment region
Nucleosome exclusion sequences
Restriction sites
Ribosome binding sites
Scaffold-attachment region
This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc.
This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression).
DNA binding sites
beta13
1.13
Repetitive elements within a nucleic acid sequence.
This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit.
Nucleic acid repeats
true
beta13
true
DNA replication or recombination.
DNA_replication_and_recombination
DNA replication and recombination
beta13
1.13
Coding sequences for a signal or transit peptide.
Signal or transit peptide
true
beta13
1.13
Sequence tagged sites (STS) in nucleic acid sequences.
Sequence tagged sites
true
1.1
true
The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
DNA-Seq
Sequencing
Chromosome walking
Clone verification
DNase-Seq
High throughput sequencing
High-throughput sequencing
NGS
NGS data analysis
Next gen sequencing
Next generation sequencing
Panels
Primer walking
Sanger sequencing
Targeted next-generation sequencing panels
Sequencing
http://purl.bioontology.org/ontology/MSH/D059014
1.1
The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
ChIP-sequencing
Chip Seq
Chip sequencing
Chip-sequencing
ChIP-seq
ChIP-exo
ChIP-seq
1.1
A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.
RNA sequencing
RNA-Seq analysis
Small RNA sequencing
Small RNA-Seq
Small-Seq
Transcriptome profiling
WTSS
Whole transcriptome shotgun sequencing
RNA-Seq
MicroRNA sequencing
miRNA-seq
This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.
RNA-Seq
1.1
1.3
DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.
DNA methylation
true
1.1
true
The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.
Metabolomics
Exometabolomics
LC-MS-based metabolomics
MS-based metabolomics
MS-based targeted metabolomics
MS-based untargeted metabolomics
Mass spectrometry-based metabolomics
Metabolites
Metabolome
Metabonomics
NMR-based metabolomics
Metabolomics
http://purl.bioontology.org/ontology/MSH/D055432
1.1
true
The study of the epigenetic modifications of a whole cell, tissue, organism etc.
Epigenomics
Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.
Epigenomics
http://purl.bioontology.org/ontology/MSH/D057890
1.1
true
Biome sequencing
Community genomics
Ecogenomics
Environmental genomics
Environmental omics
Environmental sequencing
The study of genetic material recovered from environmental samples, and associated environmental data.
Metagenomics
Biome sequencing
Shotgun metagenomics
Metagenomics
http://purl.bioontology.org/ontology/MSH/D056186
1.1
Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.
DNA structural variation
Genomic structural variation
DNA_structural_variation
Deletion
Duplication
Insertion
Inversion
Translocation
Structural variation
1.1
DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.
DNA_packaging
Nucleosome positioning
DNA packaging
http://purl.bioontology.org/ontology/MSH/D042003
1.1
1.3
A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements.
DNA-Seq
true
1.1
1.3
The alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing.
RNA-Seq alignment
true
1.1
Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions.
ChIP-chip
ChIP-on-chip
ChiP
ChIP-on-chip
1.3
The protection of data, such as patient health data, from damage or unwanted access from unauthorised users.
Data privacy
Data_security
Data security
1.3
Biological samples and specimens.
Specimen collections
Sample_collections
biosamples
samples
Sample collections
1.3
true
VT 1.5.4 Biochemistry and molecular biology
Chemical substances and physico-chemical processes and that occur within living organisms.
Biological chemistry
Biochemistry
Glycomics
Pathobiochemistry
Phytochemistry
Biochemistry
1.3
true
The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).
Phylogenetics
Phylogenetics
http://purl.bioontology.org/ontology/MSH/D010802
1.3
true
Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.
Epigenetics
DNA methylation
Histone modification
Methylation profiles
This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.)
Epigenetics
http://purl.bioontology.org/ontology/MSH/D019175
1.3
true
The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.
Biotechnology
Applied microbiology
Biotechnology
1.3
true
Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors.
Phenomics
Phenomics
1.3
true
VT 1.5.16 Evolutionary biology
The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.
Evolution
Evolutionary_biology
Evolutionary biology
1.3
true
VT 3.1.8 Physiology
The functions of living organisms and their constituent parts.
Physiology
Electrophysiology
Physiology
1.3
true
VT 1.5.20 Microbiology
The biology of microorganisms.
Microbiology
Antimicrobial stewardship
Medical microbiology
Microbial genetics
Microbial physiology
Microbial surveillance
Microbiological surveillance
Molecular infection biology
Molecular microbiology
Microbiology
1.3
true
The biology of parasites.
Parasitology
Parasitology
1.3
true
VT 3.1 Basic medicine
VT 3.2 Clinical medicine
VT 3.2.9 General and internal medicine
Research in support of healing by diagnosis, treatment, and prevention of disease.
Biomedical research
Clinical medicine
Experimental medicine
Medicine
General medicine
Internal medicine
Medicine
1.3
true
Neuroscience
VT 3.1.5 Neuroscience
The study of the nervous system and brain; its anatomy, physiology and function.
Neurobiology
Molecular neuroscience
Neurophysiology
Systemetic neuroscience
Neurobiology
1.3
true
VT 3.3.1 Epidemiology
Topic concerning the the patterns, cause, and effect of disease within populations.
Public_health_and_epidemiology
Epidemiology
Public health
Public health and epidemiology
1.3
true
VT 1.5.9 Biophysics
The use of physics to study biological system.
Biophysics
Medical physics
Biophysics
1.3
true
VT 1.5.12 Computational biology
VT 1.5.19 Mathematical biology
VT 1.5.26 Theoretical biology
The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.
Computational_biology
Biomathematics
Mathematical biology
Theoretical biology
This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).
Computational biology
1.3
true
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.
Transcriptomics
Comparative transcriptomics
Metatranscriptomics
Transcriptome
Transcriptomics
1.3
Chemical science
Polymer science
VT 1.7.10 Polymer science
VT 1.7 Chemical sciences
VT 1.7.2 Chemistry
VT 1.7.3 Colloid chemistry
VT 1.7.5 Electrochemistry
VT 1.7.6 Inorganic and nuclear chemistry
VT 1.7.7 Mathematical chemistry
VT 1.7.8 Organic chemistry
VT 1.7.9 Physical chemistry
The composition and properties of matter, reactions, and the use of reactions to create new substances.
Chemistry
Inorganic chemistry
Mathematical chemistry
Nuclear chemistry
Organic chemistry
Physical chemistry
Chemistry
1.3
VT 1.1.99 Other
VT:1.1 Mathematics
The study of numbers (quantity) and other topics including structure, space, and change.
Maths
Mathematics
Dynamic systems
Dynamical systems
Dynymical systems theory
Graph analytics
Monte Carlo methods
Multivariate analysis
Mathematics
1.3
VT 1.2 Computer sciences
VT 1.2.99 Other
The theory and practical use of computer systems.
Computer_science
Cloud computing
HPC
High performance computing
High-performance computing
Computer science
1.3
The study of matter, space and time, and related concepts such as energy and force.
Physics
Physics
1.3
true
RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.
Alternative splicing
RNA_splicing
Splice sites
This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc..
RNA splicing
1.3
true
The structure and function of genes at a molecular level.
Molecular_genetics
Molecular genetics
1.3
true
VT 3.2.25 Respiratory systems
The study of respiratory system.
Pulmonary medicine
Pulmonology
Respiratory_medicine
Pulmonary disorders
Respiratory disease
Respiratory medicine
1.3
1.4
The study of metabolic diseases.
Metabolic disease
true
1.3
VT 3.3.4 Infectious diseases
The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).
Communicable disease
Transmissable disease
Infectious_disease
Infectious disease
1.3
The study of rare diseases.
Rare_diseases
Rare diseases
1.3
true
VT 1.7.4 Computational chemistry
Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.
Computational_chemistry
Computational chemistry
1.3
true
The branch of medicine that deals with the anatomy, functions and disorders of the nervous system.
Neurology
Neurological disorders
Neurology
1.3
true
VT 3.2.22 Peripheral vascular disease
VT 3.2.4 Cardiac and Cardiovascular systems
The diseases and abnormalities of the heart and circulatory system.
Cardiovascular medicine
Cardiology
Cardiovascular disease
Heart disease
Cardiology
1.3
true
The discovery and design of drugs or potential drug compounds.
Drug_discovery
This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
Drug discovery
1.3
true
Repositories of biological samples, typically human, for basic biological and clinical research.
Tissue collection
biobanking
Biobank
Biobank
1.3
Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.
Mouse_clinic
Mouse clinic
1.3
Collections of microbial cells including bacteria, yeasts and moulds.
Microbial_collection
Microbial collection
1.3
Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.
Cell_culture_collection
Cell culture collection
1.3
Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.
Clone_library
Clone library
1.3
true
'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.
Translational_medicine
Translational medicine
1.3
Collections of chemicals, typically for use in high-throughput screening experiments.
Compound_libraries_and_screening
Chemical library
Chemical screening
Compound library
Small chemical compounds libraries
Small compounds libraries
Target identification and validation
Compound libraries and screening
1.3
true
VT 3.3 Health sciences
Topic concerning biological science that is (typically) performed in the context of medicine.
Biomedical sciences
Health science
Biomedical_science
Biomedical science
1.3
Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases.
Data_identity_and_mapping
Data identity and mapping
1.3
1.12
The search and retrieval from a database on the basis of molecular sequence similarity.
Sequence database search
Sequence search
true
1.4
true
Objective indicators of biological state often used to assess health, and determinate treatment.
Diagnostic markers
Biomarkers
Biomarkers
1.4
The procedures used to conduct an experiment.
Experimental techniques
Lab method
Lab techniques
Laboratory method
Laboratory_techniques
Experiments
Laboratory experiments
Laboratory techniques
1.4
The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data.
Data_architecture_analysis_and_design
Data analysis
Data architecture
Data design
Data architecture, analysis and design
1.4
The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data.
Data_integration_and_warehousing
Data integration
Data warehousing
Data integration and warehousing
1.4
Any matter, surface or construct that interacts with a biological system.
Biomaterials
Biomaterials
1.4
true
The use of synthetic chemistry to study and manipulate biological systems.
Chemical_biology
Chemical biology
1.4
VT 1.7.1 Analytical chemistry
The study of the separation, identification, and quantification of the chemical components of natural and artificial materials.
Analytical_chemistry
Analytical chemistry
1.4
The use of chemistry to create new compounds.
Synthetic_chemistry
Synthetic organic chemistry
Synthetic chemistry
1.4
1.2.12 Programming languages
Software engineering
VT 1.2.1 Algorithms
VT 1.2.14 Software engineering
VT 1.2.7 Data structures
The process that leads from an original formulation of a computing problem to executable programs.
Computer programming
Software development
Software_engineering
Algorithms
Data structures
Programming languages
Software engineering
1.4
true
The process of bringing a new drug to market once a lead compounds has been identified through drug discovery.
Drug development science
Medicine development
Medicines development
Drug_development
Drug development
1.4
Drug delivery
Drug formulation
Drug formulation and delivery
The process of formulating and administering a pharmaceutical compound to achieve a therapeutic effect.
Biotherapeutics
Biotherapeutics
1.4
true
The study of how a drug interacts with the body.
Drug_metabolism
ADME
Drug absorption
Drug distribution
Drug excretion
Pharmacodynamics
Pharmacokinetics
Pharmacokinetics and pharmacodynamics
Drug metabolism
1.4
Health care research
Health care science
The discovery, development and approval of medicines.
Drug discovery and development
Medicines_research_and_development
Medicines research and development
1.4
The safety (or lack) of drugs and other medical interventions.
Safety_sciences
Drug safety
Safety sciences
1.4
The detection, assesment, understanding and prevention of adverse effects of medicines.
Pharmacovigilence
Pharmacovigilence concerns safety once a drug has gone to market.
Pharmacovigilance
1.4
The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.
Preclinical_and_clinical_studies
Clinical studies
Clinical study
Clinical trial
Drug trials
Preclinical studies
Preclinical study
Preclinical and clinical studies
1.4
true
The visual representation of an object.
Imaging
Diffraction experiment
Microscopy
Microscopy imaging
Optical super resolution microscopy
Photonic force microscopy
Photonic microscopy
This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure.
Imaging
1.4
The use of imaging techniques to understand biology.
Biological imaging
Biological_imaging
Bioimaging
1.4
VT 3.2.13 Medical imaging
VT 3.2.14 Nuclear medicine
VT 3.2.24 Radiology
The use of imaging techniques for clinical purposes for medical research.
Medical_imaging
Neuroimaging
Nuclear medicine
Radiology
Medical imaging
1.4
The use of optical instruments to magnify the image of an object.
Light_microscopy
Light microscopy
1.4
The use of animals and alternatives in experimental research.
Animal experimentation
Animal research
Animal testing
In vivo testing
Laboratory_animal_science
Laboratory animal science
1.4
true
VT 1.5.18 Marine and Freshwater biology
The study of organisms in the ocean or brackish waters.
Marine_biology
Marine biology
1.4
true
The identification of molecular and genetic causes of disease and the development of interventions to correct them.
Molecular_medicine
Molecular medicine
1.4
VT 3.3.7 Nutrition and Dietetics
The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices.
Nutrition
Nutrition science
Nutritional_science
Dietetics
Nutritional science
1.4
true
The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
Omics
Omics
1.4
The processes that need to be in place to ensure the quality of products for human or animal use.
Quality assurance
Quality_affairs
Good clinical practice
Good laboratory practice
Good manufacturing practice
Quality affairs
1.4
The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines.
Healthcare RA
Regulatory_affairs
Regulatory affairs
1.4
true
Biomedical approaches to clinical interventions that involve the use of stem cells.
Stem cell research
Regenerative_medicine
Regenerative medicine
1.4
true
An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life.
Systems_medicine
Systems medicine
1.4
Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.
Veterinary_medicine
Clinical veterinary medicine
Veterinary medicine
1.4
The application of biological concepts and methods to the analytical and synthetic methodologies of engineering.
Biological engineering
Bioengineering
Bioengineering
1.4
true
Ageing
Aging
Gerontology
VT 3.2.10 Geriatrics and gerontology
The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.
Geriatrics
Geriatric_medicine
Geriatric medicine
1.4
true
VT 3.2.1 Allergy
Health issues related to the immune system and their prevention, diagnosis and mangement.
Allergy_clinical_immunology_and_immunotherapeutics
Allergy
Clinical immunology
Immune disorders
Immunomodulators
Immunotherapeutics
Allergy, clinical immunology and immunotherapeutics
1.4
true
The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.
Algiatry
Pain_medicine
Pain medicine
1.4
VT 3.2.2 Anaesthesiology
Anaesthesia and anaesthetics.
Anaesthetics
Anaesthesiology
Anaesthesiology
1.4
VT 3.2.5 Critical care/Emergency medicine
The multidisciplinary that cares for patients with acute, life-threatening illness or injury.
Acute medicine
Emergency medicine
Intensive care medicine
Critical_care_medicine
Critical care medicine
1.4
VT 3.2.7 Dermatology and venereal diseases
The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.
Dermatology
Dermatological disorders
Dermatology
1.4
The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.
Dentistry
Dentistry
1.4
VT 3.2.20 Otorhinolaryngology
The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.
Audiovestibular medicine
Otolaryngology
Otorhinolaryngology
Ear_nose_and_throat_medicine
Head and neck disorders
Ear, nose and throat medicine
1.4
true
The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism.
Endocrinology_and_metabolism
Endocrine disorders
Endocrinology
Metabolic disorders
Metabolism
Endocrinology and metabolism
1.4
true
VT 3.2.11 Hematology
The branch of medicine that deals with the blood, blood-forming organs and blood diseases.
Haematology
Blood disorders
Haematological disorders
Haematology
1.4
true
VT 3.2.8 Gastroenterology and hepatology
The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.
Gastroenterology
Gastrointestinal disorders
Gastroenterology
1.4
The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.
Gender_medicine
Gender medicine
1.4
true
VT 3.2.15 Obstetrics and gynaecology
The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.
Gynaecology_and_obstetrics
Gynaecological disorders
Gynaecology
Obstetrics
Gynaecology and obstetrics
1.4
true
The branch of medicine that deals with the liver, gallbladder, bile ducts and bile.
Hepatobiliary medicine
Hepatic_and_biliary_medicine
Liver disorders
Hepatic and biliary medicine
1.4
1.13
The branch of medicine that deals with the infectious diseases of the tropics.
Infectious tropical disease
true
1.4
The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.
Traumatology
Trauma_medicine
Trauma medicine
1.4
true
The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents.
Medical_toxicology
Medical toxicology
1.4
VT 3.2.19 Orthopaedics
VT 3.2.26 Rheumatology
The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine.
Musculoskeletal_medicine
Musculoskeletal disorders
Orthopaedics
Rheumatology
Musculoskeletal medicine
1.4
Optometry
VT 3.2.17 Ophthalmology
VT 3.2.18 Optometry
The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.
Opthalmology
Eye disoders
Opthalmology
1.4
VT 3.2.21 Paediatrics
The branch of medicine that deals with the medical care of infants, children and adolescents.
Child health
Paediatrics
Paediatrics
1.4
Mental health
VT 3.2.23 Psychiatry
The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour.
Psychiatry
Psychiatric disorders
Psychiatry
1.4
VT 3.2.3 Andrology
The health of the reproductive processes, functions and systems at all stages of life.
Reproductive_health
Andrology
Family planning
Fertility medicine
Reproductive disorders
Reproductive health
1.4
VT 3.2.28 Transplantation
The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance.
Surgery
Transplantation
Surgery
1.4
VT 3.2.29 Urology and nephrology
The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney.
Urology_and_nephrology
Kidney disease
Nephrology
Urological disorders
Urology
Urology and nephrology
1.4
Alternative medicine
Holistic medicine
Integrative medicine
VT 3.2.12 Integrative and Complementary medicine
Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.
Complementary_medicine
Complementary medicine
1.7
Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.
MRT
Magnetic resonance imaging
Magnetic resonance tomography
NMRI
Nuclear magnetic resonance imaging
MRI
MRI
1.7
The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure.
Neutron diffraction experiment
Neutron_diffraction
Elastic neutron scattering
Neutron microscopy
Neutron diffraction
1.7
Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram).
CT
Computed tomography
TDM
Tomography
Electron tomography
PET
Positron emission tomography
X-ray tomography
Tomography
1.7
true
KDD
Knowledge discovery in databases
VT 1.3.2 Data mining
The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format.
Data_mining
Pattern recognition
Data mining
1.7
Artificial Intelligence
VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)
A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only.
Machine_learning
Active learning
Ensembl learning
Kernel methods
Knowledge representation
Neural networks
Recommender system
Reinforcement learning
Supervised learning
Unsupervised learning
Machine learning
1.8
The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
Database administration
Database_management
Content management
Data maintenance
Document management
Document, record and content management
File management
Record management
This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files and reports.
Database management
1.8
VT 1.5.29 Zoology
Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation.
Animal
Animal biology
Animals
Metazoa
Zoology
Animal genetics
Animal physiology
Entomology
The study of the animal kingdom.
Zoology
1.8
The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
Protein_sites_features_and_motifs
Protein sequence features
Signal peptide cleavage sites
A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.
Protein sites, features and motifs
1.8
The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
Nucleic_acid_sites_features_and_motifs
Nucleic acid functional sites
Nucleic acid sequence features
Primer binding sites
Sequence tagged sites
Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.
Nucleic acid sites, features and motifs
1.8
Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.
mRNA features
Gene_transcripts
Coding RNA
EST
Exons
Fusion transcripts
Gene transcript features
Introns
PolyA signal
PolyA site
Signal peptide coding sequence
Transit peptide coding sequence
cDNA
mRNA
This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences.
This includes coding sequences for a signal or transit peptide. A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.
This includes regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation.
Gene transcripts
1.8
1.13
Protein-ligand (small molecule) interaction(s).
Protein-drug interactions
Protein-ligand interactions
true
1.8
1.13
Protein-drug interaction(s).
Protein-drug interactions
true
1.8
Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.
Genotyping_experiment
Genotyping experiment
1.8
Genome-wide association study experiments.
GWAS
GWAS analysis
Genome-wide association study
GWAS_study
GWAS study
1.8
Microarray experiments including conditions, protocol, sample:data relationships etc.
Microarrays
Microarray_experiment
Gene expression microarray
Genotyping array
Methylation array
MicroRNA array
Multichannel microarray
One channel microarray
Proprietary platform micoarray
RNA chips
RNA microarrays
Reverse phase protein array
SNP array
Tiling arrays
Tissue microarray
Two channel microarray
aCGH microarray
mRNA microarray
miRNA array
This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.
Microarray experiment
1.8
PCR experiments, e.g. quantitative real-time PCR.
Polymerase chain reaction
PCR_experiment
Quantitative PCR
RT-qPCR
Real Time Quantitative PCR
PCR experiment
1.8
Proteomics experiments.
Proteomics_experiment
2D PAGE experiment
DIA
Data-independent acquisition
MS
MS experiments
Mass spectrometry
Mass spectrometry experiments
Northern blot experiment
Spectrum demultiplexing
This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. Also Northern blot experiments.
Proteomics experiment
1.8
1.13
Two-dimensional gel electrophoresis experiments, gels or spots in a gel.
2D PAGE experiment
true
1.8
1.13
Northern Blot experiments.
Northern blot experiment
true
1.8
RNAi experiments.
RNAi_experiment
RNAi experiment
1.8
Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.
Simulation_experiment
Simulation experiment
1.8
1.13
Protein-DNA/RNA interaction(s).
Protein-nucleic acid interactions
true
1.8
1.13
Protein-protein interaction(s), including interactions between protein domains.
Protein-protein interactions
true
1.8
1.13
Cellular process pathways.
Cellular process pathways
true
1.8
1.13
Disease pathways, typically of human disease.
Disease pathways
true
1.8
1.13
Environmental information processing pathways.
Environmental information processing pathways
true
1.8
1.13
Genetic information processing pathways.
Genetic information processing pathways
true
1.8
1.13
Super-secondary structure of protein sequence(s).
Protein super-secondary structure
true
1.8
1.13
Catalytic residues (active site) of an enzyme.
Protein active sites
true
1.8
Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc.
Protein_binding_sites
Enzyme active site
Protein cleavage sites
Protein functional sites
Protein key folding sites
Protein-nucleic acid binding sites
Protein binding sites
1.8
1.13
RNA and DNA-binding proteins and binding sites in protein sequences.
Protein-nucleic acid binding sites
true
1.8
1.13
Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.
Protein cleavage sites
true
1.8
1.13
Chemical modification of a protein.
Protein chemical modifications
true
1.8
Disordered structure in a protein.
Protein features (disordered structure)
Protein_disordered_structure
Protein disordered structure
1.8
1.13
Structural domains or 3D folds in a protein or polypeptide chain.
Protein domains
true
1.8
1.13
Key residues involved in protein folding.
Protein key folding sites
true
1.8
1.13
Post-translation modifications in a protein sequence, typically describing the specific sites involved.
Protein post-translational modifications
true
1.8
Secondary structure (predicted or real) of a protein, including super-secondary structure.
Protein features (secondary structure)
Protein_secondary_structure
Protein super-secondary structure
Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).
Protein secondary structure
1.8
1.13
Short repetitive subsequences (repeat sequences) in a protein sequence.
Protein sequence repeats
true
1.8
1.13
Signal peptides or signal peptide cleavage sites in protein sequences.
Protein signal peptides
true
1.10
VT 1.1.1 Applied mathematics
The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models.
Applied_mathematics
Applied mathematics
1.10
VT 1.1.1 Pure mathematics
The study of abstract mathematical concepts.
Pure_mathematics
Linear algebra
Pure mathematics
1.10
The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints.
Data_governance
Data stewardship
Data governance
http://purl.bioontology.org/ontology/MSH/D030541
1.10
The quality, integrity, and cleaning up of data.
Data_quality_management
Data clean-up
Data cleaning
Data integrity
Data quality
Data quality management
1.10
Freshwater science
VT 1.5.18 Marine and Freshwater biology
The study of organisms in freshwater ecosystems.
Freshwater_biology
Freshwater biology
1.10
true
VT 3.1.2 Human genetics
The study of inheritance in human beings.
Human_genetics
Human genetics
1.10
VT 3.3.14 Tropical medicine
Health problems that are prevalent in tropical and subtropical regions.
Tropical_medicine
Tropical medicine
1.10
true
VT 3.3.14 Tropical medicine
VT 3.4 Medical biotechnology
VT 3.4.1 Biomedical devices
VT 3.4.2 Health-related biotechnology
Biotechnology applied to the medical sciences and the development of medicines.
Medical_biotechnology
Pharmaceutical biotechnology
Medical biotechnology
1.10
true
VT 3.4.5 Molecular diagnostics
An approach to medicine whereby decisions, practices and are tailored to the individual patient based on their predicted response or risk of disease.
Precision medicine
Personalised_medicine
Molecular diagnostics
Personalised medicine
1.12
Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq.
Chromatin immunoprecipitation
Immunoprecipitation_experiment
Immunoprecipitation experiment
1.12
Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time.
Genome sequencing
WGS
Whole_genome_sequencing
De novo genome sequencing
Whole genome resequencing
Whole genome sequencing
1.12
Laboratory technique to sequence the methylated regions in DNA.
MeDIP-chip
MeDIP-seq
mDIP
Methylated_DNA_immunoprecipitation
BS-Seq
Bisulfite sequencing
MeDIP
Methylated DNA immunoprecipitation (MeDIP)
Methylation sequencing
WGBS
Whole-genome bisulfite sequencing
methy-seq
methyl-seq
Methylated DNA immunoprecipitation
1.12
Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome.
Exome
Exome analysis
Exome capture
Targeted exome capture
WES
Whole exome sequencing
Exome_sequencing
Exome sequencing is considered a cheap alternative to whole genome sequencing.
Exome sequencing
1.12
true
The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions.
Design of experiments
Experimental design
Studies
Experimental_design_and_studies
Experimental design and studies
1.12
The design of an experiment involving non-human animals.
Animal_study
Challenge study
Animal study
1.13
true
The ecology of microorganisms including their relationship with one another and their environment.
Environmental microbiology
Microbial_ecology
Community analysis
Microbiome
Molecular community analysis
Microbial ecology
1.17
An antibody-based technique used to map in vivo RNA-protein interactions.
RIP
RNA_immunoprecipitation
CLIP
CLIP-seq
HITS-CLIP
PAR-CLIP
iCLIP
RNA immunoprecipitation
1.17
Large-scale study (typically comparison) of DNA sequences of populations.
Population_genomics
Population genomics
1.20
Agriculture
Agroecology
Agronomy
Multidisciplinary study, research and development within the field of agriculture.
Agricultural_science
Agricultural biotechnology
Agricultural economics
Animal breeding
Animal husbandry
Animal nutrition
Farming systems research
Food process engineering
Food security
Horticulture
Phytomedicine
Plant breeding
Plant cultivation
Plant nutrition
Plant pathology
Soil science
Agricultural science
1.20
Approach which samples, in parallel, all genes in all organisms present in a given sample, e.g. to provide insight into biodiversity and function.
Shotgun metagenomic sequencing
Metagenomic_sequencing
Metagenomic sequencing
1.21
Study of the environment, the interactions between its physical, chemical, and biological components and it's effect on life. Also how humans impact upon the environment, and how we can manage and utilise natural resources.
Environment
Environmental_science
Environmental science
1.22
The study and simulation of molecular conformations using a computational model and computer simulations.
This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc.
Biomolecular simulation
1.22
The application of multi-disciplinary science and technology for the construction of artificial biological systems for diverse applications.
Biomimeic chemistry
Synthetic biology
1.22
The application of biotechnology to directly manipulate an organism's genes.
Genetic manipulation
Genetic modification
Genetic_engineering
Genome editing
Genome engineering
Genetic engineering
1.24
A field of biological research focused on the discovery and identification of peptides, typically by comparing mass spectra against a protein database.
Proteogenomics
Proteogenomics
1.24
A biomedical field that bridges immunology and genetics, to study the genetic basis of the immune system.
Immune system genetics
Immungenetics
Immunology and genetics
Immunogenetics
Immunogenes
This involves the study of often complex genetic traits underlying diseases involving defects in the immune system. For example, identifying target genes for therapeutic approaches, or genetic variations involved in immunological pathology.
Immunogenetics
1.24
Cytometry is the measurement of the characteristics of cells.
Cytometry
Flow cytometry
Image cytometry
Mass cytometry
Cytometry
1.24
Molecular biology methods used to analyze the spatial organization of chromatin in a cell.
3C technologies
3C-based methods
Chromosome conformation analysis
Chromosome_conformation_capture
Chromatin accessibility
Chromatin accessibility assay
Chromosome conformation capture
1.24
The study of microbe gene expression within natural environments (i.e. the metatranscriptome).
Metatranscriptomics
Metatranscriptomics methods can be used for whole gene expression profiling of complex microbial communities.
Metatranscriptomics
1.24
The reconstruction and analysis of genomic information in extinct species.
Paleogenomics
Ancestral genomes
Paleogenetics
Paleogenomics
1.24
The biological classification of organisms by categorizing them in groups ("clades") based on their most recent common ancestor.
Cladistics
Tree of life
Cladistics
1.24
The study of the process and mechanism of change of biomolecules such as DNA, RNA, and proteins across generations.
Molecular_evolution
Molecular evolution
1.24
Immunoinformatics is the field of computational biology that deals with the study of immunoloogical questions. Immunoinformatics is at the interface between immunology and computer science. It takes advantage of computational, statistical, mathematical approaches and enhances the understanding of immunological knowledge.
Computational immunology
Immunoinformatics
This involves the study of often complex genetic traits underlying diseases involving defects in the immune system. For example, identifying target genes for therapeutic approaches, or genetic variations involved in immunological pathology.
Immunoinformatics
1.24
A diagnostic imaging technique based on the application of ultrasound.
Standardized echography
Ultrasound imaging
Echography
Diagnostic sonography
Medical ultrasound
Standard echography
Ultrasonography
Echography
1.24
Experimental approaches to determine the rates of metabolic reactions - the metabolic fluxes - within a biological entity.
Fluxomics
The "fluxome" is the complete set of metabolic fluxes in a cell, and is a dynamic aspect of phenotype.
Fluxomics
1.12
An experiment for studying protein-protein interactions.
Protein_interaction_experiment
Co-immunoprecipitation
Phage display
Yeast one-hybrid
Yeast two-hybrid
This used to have the ID http://edamontology.org/topic_3557 but the numerical part (owing to an error) duplicated http://edamontology.org/operation_3557 ('Imputation'). ID of this concept set to http://edamontology.org/topic_3957 in EDAM 1.24.
Protein interaction experiment
1.25
A DNA structural variation, specifically a duplication or deletion event, resulting in sections of the genome to be repeated, or the number of repeats in the genome to vary between individuals.
Copy_number_variation
CNV deletion
CNV duplication
CNV insertion / amplification
Complex CNV
Copy number variant
Copy number variation
1.25
The branch of genetics concerned with the relationships between chromosomes and cellular behaviour, especially during mitosis and meiosis.
Cytogenetics
1.25
The design of vaccines to protect against a particular pathogen, including antigens, delivery systems, and adjuvants to elicit a predictable immune response against specific epitopes.
Vaccinology
Rational vaccine design
Reverse vaccinology
Structural vaccinology
Structure-based immunogen design
Vaccine design
Vaccinology
1.25
The study of immune system as a whole, its regulation and response to pathogens using genome-wide approaches.
Immunomics
1.25
The study of the epigenetic modifications of a whole cell, tissue, organism etc.
Epistatic genetic interaction
Epistatic interactions
The study of the phenomena whereby the effects of one locus mask the allelic effects of another, such as how dominant alleles mask the effects of the recessive alleles at the same locus.
Epistasis
http://purl.bioontology.org/ontology/MSH/D057890
1.2
An obsolete concept (redefined in EDAM).
Needed for conversion to the OBO format.
Obsolete concept (EDAM)
true