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Akshay Choche
Alok Dhamanaskar
An ontology for the annotation of bioinformatics web services.
An ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.
Chaitanya Guttula
Chris Stoeckert
Jessie Kissinger
Jie Zheng
John Miller
Description
An account of the content of the resource.
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
definition
PERSON:Daniel Schober
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
imported from
For external terms/classes, the ontology from which the term was imported
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
curator note
An administrative note of use for a curator but of no use for a user
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
example
is part of
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
part of
part_of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates_in
has participant
has_participant
is concretization of
concretization of
concretization_of
concretizes
s depends on
s_depends_on
is located in
located in
located_in
is about
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
denotes
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
is_specified_input_of
Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
is_encoded_in
SWO proposed relation, link data with data format specification, or software with program language
is_encoded_of
is_executed_in
algorithm/software is_executed_in information process
is_executed_of
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
a heart
a person
a symphony orchestra
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
a surgical operation as processual context for a nosocomical infection
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a leg
an organism
substantial entity
the bottom right portion of a human torso
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
the process of cell-division
the process of sleeping
realizable entity
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
the disposition of metal to conduct electricity
the function of the reproductive organs
the role of being a doctor
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
the ambient temperature of air
the circumference of a waist
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the smell of mozzarella
trope
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
generically dependent continuant
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
a certain PDF file that exists in different and in several hard drives
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
deoxyribonucleic acids
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
ribonucleic acids
Naturally occurring polyribonucleotides.
amino acids
Carboxylic acids containing one or more amino groups.
macromolecule
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
polymer
objective specification
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
purpose of a study; support of hypothesis, discovery of new information
action specification
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
datum label
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
software
GROUP: OBI
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
data item
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Jonathan Rees
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data
symbol
20091104, MC: this needs work and will most probably change
a smallish, word-like datum...
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
directive information entity
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
algorithm
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
data format specification
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
OBI branch derived
data set
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
person:Allyson Lister
person:Chris Stoeckert
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
Person:Alan Ruttenberg
Person:Chris Stoeckart
CRID symbol
A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Bill Hogan
PMID:12345, 12345 in a database column which has header "pubmedID"
Viruses
Teleostomi
Euteleostomi
Bacteria
Homo/Pan/Gorilla group
Archaea
Eukaryota
Euarchontoglires
Simiiformes
Hominoidea
Tetrapoda
Amniota
Theria
Fungi/Metazoa group
Metazoa
Bilateria
Coelomata
Deuterostomia
Haplorrhini
Mammalia
Eumetazoa
Chordata
Vertebrata
Gnathostomata
Sarcopterygii
Craniata
Eutheria
Primates
Catarrhini
Hominidae
Homo
Homo sapiens
planned process
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Injecting mice with a vaccine in order to test its efficacy
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
A processual entity that realizes a plan which is the concretization of a plan specification.
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
organization
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
a information content entity created to indicate that information about something is not available to the person recording it.
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
A sequence data item that is about the primary structure of DNA
The part of a FASTA file that contains the letters ACTGGGAA
organism
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
plant
virus
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
sequence analysis objective
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
PERSON: James Malone
normalize objective
digital document name
A textual entity that refers to a digital document derived from a computer system.
file extension
A textual entity that is the suffix for a file name.
metadata of data format specification
A textual entity that gives the details of the different supported data formats and associated file extension and other metadata.
MIME type specification
A data format specification that is used to specify the content type over the Web. (MIME is an acronym for Multipurpose Internet Mail Extension)
clustering algorithm
An algorithm that assigns set of observations/data into subsets (called clusters) so that observations/data in the same cluster are similar in some sense.
Wikipedia: en.wikipedia.org/wiki/Nearest_neighbor_search
sequence similarity identification objective
A sequence analysis objective that describes the aim to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
pairwise sequence alignment algorithm
An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences).
multiple sequence alignment algorithm
An algorithm that is used to obtain multiple sequence alignments between nucleotide or protein sequences.
gap separation distance setting specification
ClustalW Web service Documentation and WS annotations Group, UGA
A software execution setting specification that specifies the distance between two consecutive gaps when aligning two sequences, within which introducing a new gap is penalized in addition to gap creation penalty.
end gap separation penalty setting specification
End Gap Separation: Treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above). If you turn this off, end gaps will be ignored for this purpose. This is useful when you wish to align fragments where the end gaps are not biologically meaningful.
A software execution setting specification that states whether or not to apply the gap extension penalty when scoring terminal gaps using a Boolean value. configuration parameter which is a Boolean value, that states whether or not to apply the gap extension penalty when scoring terminal gaps.
number of iterations setting specification
A software execution setting specification that specifies the maximum number of iterations to perform.
iteration strategy setting specification
A software execution setting specification that specifies the multiple alignment improvement iteration type. For clustalW, It can take values: none, tree(Iteration at each step of alignment process) or alignment(Iteration only on final alignment).
algorithm identifier
A symbol that specifies a particular algorithm to be implemented in a tool or software.
A data item which is a tree that represents the relationship between sequences and is used to build the multiple sequence alignment. For the first iteration of multiple sequence alignment process the guide tree is constructed by a clustering method while for the subsequent iterations it is constructed from the previous iteration.
Wikipedia : http://en.wikipedia.org/wiki/Multiple_sequence_alignment
retrieve alignment result objective
ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
A retrieve web service execution result objective that describes the goal of retrieving the sequence alignment result.
A CRID symbol used to uniquely identify a submitted web service execution.
multiple sequence alignment data set
A sequence alignment data set that is produced as the output of a multiple sequence alignment process.
web service execution title
A textual entity that is the name of a web service job submitted.
A web service execution that filters sequence data depending on their similarity score to a specified sequence and expectation value.
gap creation penalty setting specification
A gap penalty setting specification that specifies the penalty for introducing a new gap when producing an alignment.
DNA substitution matrix
A scoring matrix that is used for scoring alignment of nucleotide sequences.
A Matrix that stores the evolutionary distance between each pair of protein sequences, with each species starting on a new line with the species name, followed by the distances to the species in order.
compute protein evolution distance execution
A phylip execution that computes a protein evolution distance matrix using a amino acid replacement model.
gap extension penalty setting specification
A gap penalty setting specification that specifies the penalty for extending a gap when aligning sequences.
construct phylip neighbor tree execution
A phylip execution that constructs an unrooted phylogenetic tree from a protein distance matrix by successive clustering using either Neighbor joining or UPGMA method of clustering.
A web service execution that involves invocation of different programs for inferring phylogenetic relationships between groups of organisms.
http://en.wikipedia.org/wiki/Phylogenetics, http://www.phylip.com/
get web service execution status
A web service execution that returns the status (e.g. Finished, Running) of a web service execution, depending upon web service execution identifier. .
clustalW execution
A web service execution that performs multiple sequence alignment.
get supported output data format
A web service execution that retrieves all the supported output data format for a particular execution.
retrieve alignment result execution
A retrieve web service execution result that would fetch the result of alignment analysis given its unique execution identifier.
web service
A service that exposes an arbitrary set of operations which can be accessed through a programmatic interface to a web server maintained by the service provider.
Wikipedia: http://en.wikipedia.org/wiki/Web_service
There are two options for the protein weight matrix: BLOSUM and PAM. The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are. Different matrices work differently at each evolutionary distance.
A scoring matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time.
software execution
A planned process that realizes the concretization of a software.
scoring matrix
A lower triangular matrix where each cell represents a score to be assigned to a specific type of pairing of nucleotide or amino acid sequences generally used in sequence alignment.
gap penalty setting specification
A software execution setting specification that specifies the penalty value for each gap introduced when aligning sequences (accounts for both gap creation and gap extension penalties). It has little affect on the speed or sensitivity except for extreme values.
invoke software execution over network objective
An objective specification that a web service execution accomplishes.
number of match regions setting specification
A software execution setting specification that specifies the number of k-tuple matches on each diagonal used to create pairwise alignment. Decrease for speed; increase for sensitivity.
fast pairwise alignment scoring method setting specification
A software execution setting specification that specifies the output type for fast pairwise alignment score (can be either percent or absolute).
fast pairwise alignment scoring method
alignment window size setting specification
A software execution setting specification that specifies the number of diagonals around each of the 'best' diagonals that will be used for joining word matches. Decrease for speed; increase for sensitivity.
alignment word size setting specification
A software execution setting specification that specifies the alignment word size used to find matches between the sequences. A higher value increases the speed of the alignment but decreases the sensitivity.
multiple sequence alignment objective
A sequence similarity identification objective that aims to align multiple sequences at a time to determine the equivalence between them.
pairwise sequence alignment objective
A sequence similarity identification objective that aims to align two sequences at a time to determine the equivalence between them.
number of top combinations setting specification
A software execution setting specification that specifies the number of HSPs to be reported, such that any given HSP is allowed to be a member of just one set. Values: a numerical value or 'All'
pairwise alignment sensitivity setting specification
A software execution setting specification that specifies the sensitivity level of the search performed, it can take following values (very low, low,normal, medium, high).
pairwise alignment statistical model setting specification
A software execution setting specification that specifies a statistical model to use for scoring alignments (pairwise). Can take values from (sum p, Poisson, kap).
pairwise alignment data format specification
A data format specification that specifies the format for the data produced as a result of pairwise sequence alignment. e.g. BLASTXML
low complexity sequence filter algorithm identifier
A sequence filter algorithm identifier that specifies an algorithm to pre-process the query sequence, such that the low complexity regions in the sequence are filtered out before sequence alignment as low complexity regions tend to give a false estimate of the similarity score.
A data item which specifies a sequence filter that pre-processes the query sequence before alignment to remove the undesired portions of it.
inclusion of filtered sequences setting specification
A software execution setting specification that specifies whether or not to show in the output file the query sequence used for the search, post filtering. Filtering here refers to masking of low complexity regions.
maximum match score setting specification
A software execution setting specification that specifies the maximum number of match scores displayed in the output.
A software execution setting specification that defines the range of query sequence to use for search.
maximum number of matched alignments setting specification
A software execution setting specification that specifies the maximum number of alignments displayed in the output.
A textual entity that specifies the DNA strand, upper, lower or both of a specific gene to be considered in alignment.
A software execution setting specification that determines the minimum allowable score for a sequence to be matched after which the algorithm gives up on aligning that sequence.
A data set that is stored on a computer and used for molecular sequence similarity search.
pairwise alignment hits ordering setting specification
A software execution setting specification that specifies the ordering criteria that is used to order the sequences (before displaying) that matched the search criteria. For example : The results could be ordered by the expectation value of sequences or using some other quantity like their score.
A sequence data that is about sequence of amino acids which are linked by peptide bonds.
A symbol used to identify (uniquely for a particular web service) the output type.
A quantitative confidence value which determines a threshold value such that only alignments scoring more than this value are considered.
A retrieve web service execution result that retrieves the outcome of a signal peptide prediction process given a unique web service execution identifier.
A web service execution that performs local pairwise sequence alignment to search a database for similar sequences.
It is getting inferred as a Sequence alignment data Transformation is that what we want
A protein signature prediction method that serves as a prediction model to predict the location of signal peptides in a protein sequence.
A data set that is as an outcome of protein signature prediction process.
BLAST (Basic Local Alignment Search Tool), a pairwise sequence alignment algorithm is a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold.
pairwise sequence alignment data transformation
A data transformation process that attempts to align two molecular sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
EDAM: alignment & WS Annotations Group, UGA
local pairwise sequence alignment data transformation
A pairwise sequence alignment data transformation that attempts to align two molecular sequences considering only parts of the sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
global multiple sequence alignment data transformation
A multiple sequence alignment data transformation that attempts to align the sequences considering their entire length.
check web service execution status objective
An objective specification that describes the goal of fetching the status of a web service execution.
A record of missing knowledge that describes terms in the document that are not present in the ontology.
match mismatch scores setting specification
A software execution setting specification that specifies the scores for a match and miss-match, to be used when searching for similar nucleotide sequences.
A local pairwise sequence alignment data transformation that performs pairwise sequence alignment to search sequence databases for similar sequences.
A CRID symbol that serves as an identifier for a molecular sequence or for an entry from a molecular sequence database.
A software execution setting specification which specifies whether the gapped areas in query sequence should be aligned in the process of sequence alignment or not using a Boolean value.
Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29
A data set that is made up of a rectangular array of elements (or entries) set out by rows and columns.
A web service execution that retrieves the sequence given the sequence identifier and the sequence database that has the sequence.
An identify protein signature execution that attempts to predict the presence and location of signal peptide cleavage sites in a protein sequence.
predict signal peptide cleavage sites objective
An identify protein signature objective that describes the goal of predicting the presence and location of signal peptide cleavage sites in an amino acid sequence.
A software execution that is provided by the web service, and involves invoking software execution over network.
A data format specification for molecular sequence feature information.
An objective specification of retrieving a sequence from a sequence database given the sequence identifier and the database that has the sequence.
display histograms setting specification
A software execution setting specification that is used to specify whether histogram is returned with the result of FASTA search using true or false Boolean value. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.
slow pairwise sequence alignment data transformation
A pairwise sequence alignment data transformation that produces accurate alignments are carried out by using a dynamic programming method (Myers and Miller) to align every pair of sequences.
multiple sequence alignment data transformation
A data transformation that attempts to align multiple (more than two) molecular sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
A matrix with equal number of rows and columns for which all the elements above the main diagonal have values equal to 0.
A data set that is produced as the output of some sequence alignment process.
sequence alignment data format specification
A data format specification that specifies the data format for the outcome of sequence alignment (pairwise or multiple) process.
multiple sequence alignment data format specification
A data format specification that specifies the format for the data produced as a result of multiple sequence alignment. e.g. FASTA, PHYLIP, ALN W/Numbers
order of sequences in alignment setting specification
A software execution setting specification that designates the order in which sequences appear in a final alignment. If ALIGNED option is chosen, the output order will be the order in which the sequences were aligned (from the guide tree/dendrogram). If INPUT option is chosen, the output will be in the same order as the input sequences.
web service execution status
A symbol that is used to specify the status of a web service execution. It usually takes one of following values - DONE, ERROR, NOT_FOUND,PENDING, RUNNING
ClustalW Web service Documentation www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
fast pairwise sequence alignment data transformation
A pairwise sequence alignment data transformation that produces Fast/Approximate alignments using the method of Wilbur and Lipman (1983) and may be more suitable for sequences longer than 1000 residues.
are local, fast and slow pairwise alignments disjoint
An objective specification that describes the goal of filtering sequence data depending on their similarity score to a specified sequence and expectation value.
retrieve signal peptide result objective
A retrieve web service execution result objective that describes the goal of retrieving the result of an operation to predict the presence and location of signal peptide cleavage sites in amino acid sequences.
display multiple HSPs setting specification
A software execution setting specification that specifies whether multiple high scoring alignments have to be displayed or not in the result using true or false Boolean value.
retrieve supported output data format objective
An objective specification that describes the goal of retrieving the supported output data formats for a particular web service execution.
A MIME type specification which represents an encoding scheme that represent binary data in an ASCII string format by translating it into a radix-64 representation.
EBI online courses : http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/what-are-protein-signatures
An algorithm or a predictive model to predict the presence of a particular protein signature.
A web service execution that fetches the outcome of some previously executed web service operation (execution) given an execution identifier that is unique for that particular web service.
A data item which is a score assigned for a signal peptide region predicted by a signal peptide prediction algorithm.
signal peptide prediction threshold value
A quantitative confidence value that acts as a threshold score to determine if the sequence pattern in consideration is a signal peptide or not.
A web service execution that tries to locate occurrence of different known protein signatures like signal peptides in a protein sequence.
InterPro Documentation at EBI : ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/FAQs.html
software execution setting specification
An information content entity which is an input setting parameter (usually optional) to some software execution that controls the way in which output is generated or displayed or which algorithm need to be executed.
SignalP Web service documentation / ITPPR
A data item which is the outcome of predict signal peptide cleavage sites execution that specifies if a signal peptide chain is found or not.
comma separated values data format specification
A data format specification that consists of any number of records and each record separated by a comma (',').
An objective specification that describes the goal of identifying protein signatures in a protein sequence.
retrieve web service execution result objective
An objective specification that describes the goal of retrieving the outcome of some previously executed web service execution.
predicted signal peptide cleavage sites data set
A predicted signal peptide cleavage sites data set that includes the outcome and all the meta data of signal peptide cleavage sites prediction process.
A web service execution identifier that uniquely identifies a submitted a phylip web service execution.
Check how much it effect Suggestion..!! Obsolete it.!
A sequence analysis objective that describes the goal of constructing a phylogenetic tree that shows inferred evolutionary relationships between protein sequences.
An algorithm that is the method for construction of consensus tree.
A data set which is a tree that represents evolutionary relationships between species, where the length of branches of the tree can signify evolutionary distance.
evolution based amino acid substitution matrix
An amino acid substitution matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time calculated using an empirical model for protein evolution.
compute protein evolution distance objective
A sequence analysis objective that aims to compute a protein distance matrix for a multiple sequence alignment using a suitable amino acid replacement model.
A phylogenetic tree that is a cladogram which summarizes agreement between two or more phylogenetic trees.
A data set that is a set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences).
A phylip execution that constructs a consensus tree that summarizes the agreement between two or more phylogenetic trees.
transcript sequence data
A RNA sequence data that is about the primary structure of RNA sequence produced by transcription.
ITPPR
Predicted RNA/mRNA Sequence (introns spliced out).
minimum signalp D score setting specification
A software execution setting specification that specifies the minimum value of D-score which is the average of the S-mean and Y-max score from SignalP-NN (neural network).
min sigp D score
minimum signalp sum score setting specification
A software execution setting specification that specifies the minimum value of signalP summary conclusion score. SignalP-NN (neural network) provides four scores and a conclusion for each such that the conclusion is 1 if the score meets a certain criteria and 0 otherwise. The SignalP summary conclusion is the sum of the four conclusions generated by SignalP, thus four is the highest score possible. We consider a summary conclusion score of three to be significant.
min sigp sum score
minimum signalp probability setting specification
A software execution setting specification that specifies the minimum value of signal probability from SignalP-HMM.
min sigp signal probability
any or all signalp setting specification
A software execution setting specification that specifies Union or intersection of advanced parameters.
find genes objective
An objective specification of retrieving genes based on different parameters (e.g., gene locus tag, taxonomy or signal peptide etc.).
find genes by taxonomy execution
A web service execution that retrieves all genes of one or more species/organism(s).
gene locus tag
A CRID symbol that is systematically applied to every gene in a genome within the context of sequencing projects.
EMBL-EBI
RNA sequence data
A sequence data that is about the primary structure of RNA.
coding sequence data
A sequence data that is about primary structure of coding sequence of DNA.
Coding Sequence
protein sequence length
A data item that represents length of predicted protein sequence.
Protein Length.
find genes using signal peptide execution
A web service execution that retrieves all genes that are predicted to encode a signal peptide.
genomic location of gene
A data item indicates the location of a gene in the genome, which can influence the expression of the gene and functional interactions of the gene expression products.
CBIL-UPENN
For a gene identified by gene locus tag TGME49_039250 the corresponsing genomic location of the gene would be TGME49_chrVI: 484,995 - 494,025 (-) where 484,995 is the starting position and 494,025 is the end position of the gene in the genome data.
location text
find genes by locus tag execution
A web service execution that retrieves genes using list of comma separated gene locus tag.
maximum isoelectric point setting secification
A software execution setting specification that specifies the upper bound for the protein isoelectric point.
maximum isoelectric point
minimum number of predicted transmembrane domains setting specification
A software execution setting specification that specifies the lower bound on number of predicted transmembrane domains a protein may have.
minimum number of predicted transmembrane domains
minimum isoelectric point setting specification
A software execution setting specification that specifies the lower bound for the protein isoelectric point.
minimum isoelectric point
epitope confidence setting specification
A software execution setting specification that specifies the confidence of epitope present in predicted protein for a gene. This parameter can have combination High, Medium or Low as values.
The epitope confidence can be specified as High, Medium or Low.
epitope confidence
find genes by transmembrane domain execution
A web service execution that retrieves all genes having number of predicted transmembrane domains in a range that user specify.
find genes by transmembrane domain
find genes with epitopes execution
A web service execution that retrieves all genes whose encoding protein has an epitope identified by the Immune Epitope Database and Analysis Resource with the confidence specified by the user.
find genes with epitopes
find genes by molecular weight execution
A web service execution that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify.
find genes by molecular weight
minimum molecular weight setting specification
A software execution setting specification that specifies the minimum value for protein molecular weight.
minimum molecular weight
maximum molecular weight setting specification
A software execution setting specification that specifies the maximum value for protein molecular weight.
maximum molecular weight
maximum number of predicted transmembrane domains setting specification
A software execution setting specification that specifies the upper bound on number of predicted transmembrane domains a protein may have.
maximum number of predicted transmembrane domains
find genes by isoelectric point execution
A web service execution that retrieves all genes whose protein product has an isoelectric point in a range that user specify.
find genes by isoelectric point
region
primary structure of sequence macromolecule
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
polypeptide
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
polymer_attribute
An attribute to describe the kind of biological sequence.
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
PAM
BLOSUM62
absolute
percent
A BLAST algorithm that searches/aligns a protein query sequence against a protein database at a protein level.
A BLAST algorithm that searches/aligns a nucleotide query sequence against a protein database at a protein level.
A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level.
A BLAST algorithm that searches/aligns a protein query sequence against a nucleotide database at a protein level.
A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a protein level.