The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata.
Genomic Epidemiology Ontology
metadata section
term as in existing standard
term source
The user interface label is the label that should be placed on a datum when presented on a form or report
user interface label
user interface definition
A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used.
user interface help
user interface hidden
A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report
user interface feature
This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc.
obsolete: user interface value specification
UI regex normalize
user interface regular epression normalize
UI regex validate
user interface regular expression validate
UI regex format
user interface regular expression display format
part of
Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions.
realized in
obsolete has string specification of
T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2)
Damion Dooley
Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way.
after
obsolete: has string value specification
obsolete: has categorical specification of
obsolete: has categorical value specification
has unit
is about
specifies
inheres in
aligned with
T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
has component
has input
has output
output of
link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
exactMatch
An object relation between a LinkML SlotDefinition to a LocalName.
An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.
Notes and comments about an element intended for external consumption.
Date/time at which the element was created.
Not Applicable; Missing; Not Collected; Not Provided; Restricted Access
A value (string or URI) indicating the data collection state an instance of a slot has.
A description of the element's purpose and use
A list of terms from different schemas or terminology systems that have identical meaning.
Id of the schema that defined the element.
The imports entry that this element was derived from. Empty means primary source
The ncname of the source of the name.
local_name_source
A name assigned to an element in a given ontology.
For slots with ranges of type number, the value must be equal to or lowe than this
For slots with ranges of type number, the value must be equal to or higher than this
true means that slot can have more than one value
The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class.
The string value of the slot must conform to this regular expression
A list of possible values for a slot range.
true if this slot is not required, but is recommended.
true means that the slot must be present in the loaded definition.
A reference.
IAO:0000122 ('ready for release')
status of the element.
The uri that defines the possible values for the type definition
URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)
Description of what the value is doing.
The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
A persistent, unique identifier of a molecular sequence database entry.
sequence accession
The name of a field in a database.
database field name
NCCLS
National Committee on Clinical Laboratory Standards (NCCLS)
On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI
order: ARO:3004303 # nonsensitive ARO:3004300 # intermediate ARO:3004302 # sensitive ARO:3004304 # sensitive - dose dependant ARO:3004301 # resistant
Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface.
deoxyribonucleic acid
obsolete: antibiotic
pyrazinamide
Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role.
K antigen
isoniazid
Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role.
specimen extraction matrix
"This observable is important where process of capturing sample can affect dna extraction."
state / province / territory / region
Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water.
common vehicle transmission
A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken)
condition
medical condition
medical state
Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed.
Condition
The process of drawing in by breathing.
inhalation
Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
MIxS
A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness
symptom onset date
A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure.
foodon product type
food packing medium
[Oceans and Seas]
Census Regions and Divisions are groupings of States that subdivide the United States.
United States Census Bureau
A census region in the United States of America
directly governed city (North Korea)
GSCID-BRC standard
The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases.
The NIAID page for specifications has a broken link for Core Project. This is the existing page: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project Link page is: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards
This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists.
GSCID-BRC Project and Sample Application Standard
MIxS standard
MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC)
Minimum Information about any (x) Sequence (MIxS)
MIMARKS standard
The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences.
Minimum information about a marker gene sequence
"other (metadata choice)" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed.
This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information.
other (metadata value)
other relevance
other
Other: specify the sample scope that was used.
other specimen scope
other material
Other: specify the material that was used.
other material derived from specimen
"other capture type" is a free text description provided to indicate a target capture specification not covered by the other types.
other capture type
Specify the project method
other project method
This is an organizational category for grouping parameters relevant to a biomedical sample.
obsolete: draft GenEpiO BioSample standard
An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records.
obsolete: NCBI antibiogram data item
HIPPA PHI guideline
The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - the individual’s past, present, or future physical or mental health or condition, - the provision of health care to the individual, or - the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above."
American HIPPA Protected Health Information (PHI) guidelines
The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen.
obsolete: subject species
NCBI BioSample: intersex
obsolete: intersex
obsolete: isolation date
A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture
culture isolation date
year/month/day
A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation.
culture frozen date
isolate received date
date the isolate was entered into the database
isolate upload date
gut, spine, tongue, lung
Name of body site where the specimen was obtained from, such as a specific organ or tissue.
Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise.
subject anatomical site
order: NCIT:C115935 # healthy NCIT:C25610 # pathologic NCIT:C28554 # deceased
Health or disease status of a given subject at time of specimen collection.
Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future.
subject health status at time of specimen collection
Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.
specimen source context
Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from.
subject body product
Please refer to the definitions of depth in the environmental packages
collection depth datum
The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
obsolete: specimen source environmental material
A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen.
Gender is not used because it is a term referencing human social and cultural convention.
subject sex specification
descriptive; type of human use (park, farm, urban)
Human use of land involving the management and modification of natural environment or wilderness into built environment.
URI: http://en.wikipedia.org/wiki/Land_use
specimen collection site land use
Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens.
URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf
fecal indicator bacteria count
GMI MDM standard
The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records.
the Global Microbial Identifier Minimum Data for Matching (MDM) Standard
soluble organic material name;measurement value
concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
soluble inorganic material
soluble inorganic material concentration
total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus
Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway).
stream order categorical measurement datum
OD reading or cfu's or cells per millilitre
Restriction enzyme for first characterization
primary enzyme (LMAAI)
PFGE test specification
First PFGE pattern from given diagnostic restriction enzyme
PFGE primary test
Restriction enzyme for second characterization
secondary enzyme (LMACI)
Second PFGE pattern from given diagnostic restriction enzyme
PFGE secondary test
inferred from BCCDC interviews and Bionumerics
Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7
URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp
Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST).
The process of fingerprinting the core genome of a bacteria.
Add under upcomming OBI "DNA fingerprinting assay".
Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains.
16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.
URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html
pathogenic shiga toxin produced by STEC E. coli
Stx toxin type datum
Stx toxin subtype datum
level of Stx1 toxin derived tissue culture toxicity
level of Stx2 toxin derived tissue culture toxicity
An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture.
Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result.
AccuProbe culture identification assay
An AccuProbe reagent kit for identifying Listeria monocytogenes.
URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf
AccuProbe Listeria monocytogenes culture identification reagent kit
A categorical diagnostic result of an AccuProbe test.
Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product.
This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria
an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species.
Qualicon (DuPont) RiboPrinter Microbial Characterization System
a library of RiboPrinter recognised patterns
DuPont identification number from the DuPont identification library
The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup.
Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter
Date the sequencing run was performed
sequencing run date
location the sequencing run was performed
Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI
A sequencing plaform (brand) is a name of a company that produces sequencer equipment.
sequencing platform (brand)
the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline.
the sequencing application is the use or purpose of the sequencing
sequencing application
the sequencing conditions and the analyte being measured
obsolete: sequencing assay
lab method to determine the order of nucleotides in a DNA molecule
sequencing chemistry
A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets.
obsolete: GSCID-BRC data item
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
sequencing run multiplex identifiers
Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf
1,2,3, AX234, etc.
A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis.
PulseNet: SubmittedNumber
sample name
sample title
sequencing run sample identifier
Number of sequencing chemistry cycles
sequencing count of chemistry cycles
Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications.
sequencing kit
A string datum which is the version/configuration of the reagent cartidge.
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
adapter sequence
The removal of adapter sequences from demultiplexed data reads
read adapter trimming
Illumina metagenomic protocol (part 15044223), with Nextera
Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.
GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html
The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period.
number of expected base pairs per genome
Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6.
URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html
Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density.
URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf
percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly
URI: http://en.wikipedia.org/wiki/Phred_quality_score
the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation
Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used.
from within "Finishing strategy" in GROUP: MIxS
"Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices.
CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237.
assembly status
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
URI: http://en.wikipedia.org/wiki/Shotgun_sequencing
Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G"
A contig count is the count of contigs that belong to a sequence assembly.
contig count
Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
assembly name (identifier)
For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
obsolete: NCBI BioSample data item
An NCBI BioProject data item is a datum within the NCBI BioProject standard collection
obsolete: NCBI BioProject data item
The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform.
obsolete: INSDC MDM standard
A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard.
obsolete: MIxS data item
The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity.
draft data standard
obsolete: HIPPA PHI data item
obsolete: PulseNet data item
The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to.
Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf
I2B2 Data Protection role standard
order: NCIT:C115935 # healthy NCIT:C25610 # pathologic / diseased NCIT:C28554 # deceased
A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields.
subject health status (GSCID-BRC)
The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard
GSCID-BRC Core Sample standard
A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard.
GSCID-BRC Core Project standard
Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens.
specimen category
Age unit of the age measurement of a subject (individual organism).
Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't.
subject age - unit
The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases.
National Center for Biotechnology Information standard
NCBI standard
A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event.
Adapted from NIAID GSCID-BRC metadata working group
Note that this is expressed in a particular format in some standards.
specimen collection location - city or region
The country of the site of a given specimen collection event.
NIAID GSCID-BRC metadata working group
specimen collection location - country
The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries.
Darwin Core Terms
A datetime measurement related to a person's travel with respect to potential epidemilogical implications.
travel history item
The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations.
travel start date
The date of a person's return to some residence from a journey originating at that residence.
travel end date
Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip.
infection aquired during travel
This is a model of the datums involved in an epidemiology investigation.
draft pathogenic epidemiology case investigation record
The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc.
draft pathogenic epi case exposure record
A description of a food item that a case patient has come in contact with.
draft pathogenic epi case food record
food brought back from travel
An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation.
epidemiology contact network model
An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen.
epi contact network model - human
This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal.
epi contact network model - animal
A note is text that provides human-readable information on one or more subjects.
note
An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics.
draft pathogenic epi case general information record
A record of the details around how, when, and from what an isolate was extracted.
draft pathogenic epi case isolate detail record
A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted.
specimen source substance
An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process.
isolate sequence filename
A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms.
cluster identifier
A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease.
draft pathogenic epi case test record
A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen.
contact specification - lab test requester
A food cultural origin datum indicates the cultural origin of a food product.
food cultural origin
A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event.
draft pathogenic epi case travel record
Region (England) (entry subject to GAZ replacement)
An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation.
contact specification - epi network contact
This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data.
public health lab epidemiology contextual data standard
This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates.
draft whole genome sequencing lab test record
draft WGS lab bioinformatics process record
draft WGS lab sequencing record
An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record.
NCBI SRA meta information standard
An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay.
isolate raw read filename
The version identifier of a packaged kit tailored for specific sequencing workflows.
library preparation kit version
The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads.
read trimming and filtering software
bioinformatics pipeline name
bioinformatics pipeline version
bioinformatics pipeline protocol
draft WGS lab sequencing quality metrics record
draft WGS lab assembly quality metrics record
A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects).
Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types"
project data type
Genome assembly project utilizing already existing sequence data including data that was submitted by a different group
assembly project
A sequencing project involving clone-ends
clone ends project
A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets
epigenomics project
Exome resequencing project
exome resequencing project
A whole, or partial, genome sequencing project (with or without a genome assembly)
genome sequencing project
The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb.
draft ReSeq Tuberculosis data platform standard
In expressions like: "<= 8mg/L"
The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold.
test threshold measurement comparator
The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration.
less than
The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration.
less than or equal to
The "equal to" comparator indicates that a given substance was present at the given quantity or concentration.
equal to
The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration.
greater than or equal to
The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration.
greater than
order: OBI:0001616 # specimen identifier OBI:0001614 # GenBank ID GENEPIO:0001100 # antibiogram drug test model GENEPIO:0002062 # amr testing reference standard GENEPIO:0002045 # amr resistance testing method GENEPIO:0002047 # ... version or reagent GENEPIO:0002049 # amr testing platform GENEPIO:0002056 # ... vendor
The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records.
NCBI Antibiogram standard
obsolete: NCBI isolate AMR testing model
A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money.
obsolete: restaurant
iPHIS standard
The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions.
Canadian Integrated Public Health Information System (iPHIS) Standard
The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci.
The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171
MIRU24 - international standard
The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different.
The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156
MIRU24 - Canadian standard
spray-wading water
pool water
obsolete: hot tub
A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school.
obsolete: cafeteria
obsolete: bakery
A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods.
obsolete: delicatessen
A food kiosk is a kiosk (a booth with an open window on one side) that sells food.
obsolete: food kiosk
A grocery store is a retail store that primarily sells food.
obsolete: grocery store
A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin.
obsolete: specialty/ethnic store
A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods
obsolete: market
A time measurement datum that pertains to a patient's medical treatment.
treatment history datum
A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere
obsolete: take out restaurant
A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient.
treatment start date
canoeing / kayaking / boating
hiking
camping
obsolete: social gathering
obsolete: party
obsolete: wedding
obsolete: baby shower
obsolete: potluck
obsolete: community event
A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living.
obsolete: long term care facility
A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient.
treatment end date
food related exposure event
Some bacteria are associated with particular foods. Need relationship
infection-specific food detail
A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis.
tuberculosis treatment drug
“Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf
vegetarian
A time measurement datum that pertains to an organism's physical location.
organism location history datum
This will take on a sub-herarchy of food types.
food avoidance
special diet
water related exposure event
municipal water
A time measurement datum indicating the year a person immigrated to a given country.
immigration year of arrival
bottled water
An event (occuring at some location and for some duration of time) where
infectious disease exposure event
human related exposure event
animal related exposure event
Identification or description of the specific individual from which this sample was obtained
NCBI BioSample isolate (human name or description)
obsolete: petting zoo
agricultural fair
An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used.
isolate passage history datum
For Eschericia coli: STEC, UPEC
A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host
NCBI pathotype
pet treat
pet food (raw)
An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation.
human exposure event - travel datum
boat / cruise travel
train travel
bus travel
car travel
airline travel
A travel mode is a type of transportation which a given human has used while travelling on a particular trip.
travel mode
A travel reason is a motivation for traveling on a particular trip expressed by the traveller.
travel reason
travel for pleasure
business activity
religious missionairy activity
rural backpacking activity
visiting relative/friends
travel tour
unsure of travel reason
The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting.
draft tuberculosis - specimen contextual data standard
behavioural risk factor
obsolete: E. coli serotype part
O antigen
H antigen
homeless status
A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level
serovar/serotype common name
Salmonella serovar
Salmonella serovar name
Salmonella antigenic formula
drug use status
incarceration status
HIV status
HIV risk status
A.I.D.S status
drug abuse status
injection drug use status
recreational drug use status
methadone use status
substantial alcohol use/abuse status
smoking status
A country of birth is the country that a given person (or animal) was born in.
country of birth
Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) 13 (with respect to a ReSeqTB SNP pipeline sample report)
A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset.
sequence number
The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive.
date last seen alive
second line or reserve tuberculosis drug
tuberculosis infection anatomical site
obsolete: NCBI Antibiogram model
order: GENEPIO:0001187 # antimicrobial resistance test drug GENEPIO:0002112 # drug MIC GENEPIO:0002080 # drug minimum inhibitory concentration unit GENEPIO:0001001 # measurement comparator NCIT:C85539 # antimicrobial resistance phenotype GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF
This is the minimal set of parameters for drug test results for a particular antimicrobial agent.
draft antibiogram drug test model
A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time.
predicted exposure start
A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time.
predicted exposure end
Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc.
map project
Metagenome: sequence analysis of environmental samples
metagenome project
Metagenome assembly: a genome assembly generated from sequenced environmental samples
metagenome assembly project
Other: a free text description is provided to indicate Other data type
other project data type
Phenotype or Genotype: project correlating phenotype and genotype
phenotype or genotype project
Proteome: large scale proteomics experiment including mass spec. analysis
proteome project
Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material.
random survey project
Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing
targeted locus (loci) project
Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray.
transcriptome or gene expression
A sequencing project with a primary goal of identifying large or small sequence variation across populations.
variation project
(Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)?
help: Consult the http://www.insdc.org/country.html country list for valid options.
The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver".
INSDC country qualifier
phenotype
Phenotype: phenotypic measurements for submission to dbGaP
phenotype project objective
genome material
genome material from specimen
TB lineage 7 - Ethiopia
An object aggregate which has as members whole organs or parts of organs, possibly from different organisms.
organs or organ parts
A travel destination which a given human has travelled to on a particular trip and is outside Canada.
travel outside Canada
A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest.
travel outside province/territory
An instance of a "data field category" that contains the "bioproject accession field", "biosample accession field", and "GISAID accession field".
A data field category which receives a range of one or more data fields.
data field category
A livespan history item is a date-associated event pertaining to the life of a subject.
lifespan history item
untreated water
treated water - ambient temperature
epidemiology investigation data item
Unclear semantics and origin
obsolete distribution event
obsolete supply point / event
well water - treated
organism datum
a role which inheres in an organism and is realized by the process of being alive
organism role
isolate organism role
animal role
taxonomic datum
A course of treatment designed to resolve an infectious disease
infectious disease treatment
This is a collection of drugs used to test antimicrobial resistance.
This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt
antimicrobial resistance test drug
Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms.
analytic datum
obsolete: type of illness
A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen
specimen with confirmed presence of disease agent
dietary restriction
A person which has a patient care role.
patient type
obsolete: mother
A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient)
Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes.
subject disease outcome
treated water - warm/hot
jacuzzi water
whirlpool water
A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen
patient as host datum
pregnancy history item
date of conception
lifespan history record
obsolete: food cooking method
obsolete: food preservation method
infectious disease case datum
laboratory data
specimen record
The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material.
specimen type (host or environmental context)
specimen source material category
Organism has a symbiotic relationship with host
symbiotic role
obsolete: NCBI BioSample attribute package
obsolete: host sample material
food specimen detail
patient specimen
environmental
NCBI Biosample: environmental (swab or sampling)
environmental specimen
A specimen extracted from an animal
animal specimen
built environment specimen
food specimen
natural environment specimen
The type of person a patient had epidemiological (i.e. close proximity) contact with.
exposure event person
An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen.
exposure group statistics record
symptom history item
health state record
obsolete: swab
[WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate
obsolete: fluid - aspirate
Plant rinse is a rinse derived from plant material from one or more plants.
plant rinse
outbreak animal exposure event location
animal exposure process
animal exposure event by material
exposure by human contact
unnecessary distinction
obsolete: human exposure activity type
outbreak human exposure event location
A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers.
human to human exposure process
water exposure by source
human water activity
This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example.
health authority
order: HP:0000118 # symptom FLU:0000976 # onset GENEPIO:0001789 # cessation GENEPIO:0001784 # duration
symptom record
A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate.
PFGE pattern
phage type salmonella (DT)
phage type e-coli 0157 (PT)
sequence record
A type of built structure that is suspected to be related to an outbreak investigation.
outbreak exposure event location
lab test history record
obsolete: earth surface
A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts.
A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status.
data specification
A specimen history item is a time-related datum about a particular specimen
specimen history item
diagnostic test
obsolete: sample datum
A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate.
obsolete: laboratory sequencing datum
genomic sequencing annotation datum
ISSUE: lab test results are appropriate to lab test types. Logic around that?
lab test record
sequencing assembly datum
A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results.
container record
identifier of a person with the context of a health care system
health care personal identifier
A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to.
strain identifier
A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient.
line list object
This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues.
awaiting ontology review
The IRIDA user ID is a user account identifier provided by the IRIDA.ca system.
The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen
exposure group healthy count
The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen
exposure group ill count
human general activity
An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value.
exposure history record
isolate history record
An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet).
outbreak history record
Needs to cover the various pregnancy events
pregnancy history record
Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation.
diagnosis record
exposure event record
hospitalization event record
exposure history item
hospital admission date
A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly.
exposure event end
A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly.
This datum is NOT predicted as a function of pathogen and first symptom date.
exposure event start
hospitalization history item
isolate history item
outbreak history item
hospital discharge date
A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines.
notification date
An outbreak date is on which disease onset appears to have occured
outbreak date
An outbreak over date is the date on which a disease outbreak appears to have abated
outbreak over
test history item
lab test result date
A data item that is a set of entities, referenced by mention, that don't necessarily have something in common.
While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common.
data enumeration
An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition.
signs & symptoms
A particular attribute (feature, quality or process history) of a food sample.
The underlying facets will be supplied from the FoodOn food ontology.
food specimen datum
order: FOODON:03411564 # food source FOODON:00002381 # food product by organism FOODON:03311737 # processed food product NCIT:C71898 # brand name
A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products.
food specimen specification
An agency that has reported a disease cluster.
disease cluster notification agency
This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects
obsolete: NCBI BioProject ID
The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen.
exposure group unknown health status count
A role which inheres in a person and is realized by the process of being in the context of civilization
person role
An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine.
exposed person role
parent-guardian role
illness causality
pre-existing condition
To restore to the normal state after some pathologic process.
Dorland's Illustrated Medical Dictionary, 30th ed.
improving
recovering
resolving health trend
close interpersonal relationship exposure
Found to be redudant with another term, deprecrated in favor of said term.
exposure to individual with diarrhea
other human exposure
sexual contact exposure
exposure via diaper changing (human fecal)
container identifier
outbreak identifier
GENEPIO
reference genome size
The assembly genome size is the sum of all lengths of a sequence assembly's contigs.
As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. "
assembly genome size
Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community
reference genome identifier
Assembly QC
The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. The formula: | (reference_genome_size - assembly_genome_size) | / reference_genome_size This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample.
genome size delta ratio
This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome.
genome size delta ratio QC threshold
The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome.
contig N50 length QC threshold
The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length.
contig N99 length QC threshold
Homo sapiens
The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens".
subject organism (host) taxonomic species
A single datum having to do with a metric for genomic sequence assembly quality control. A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does.
assembly quality control datum
GSCID-BRC:Clinical/host-associated pathogen
clinical or host-associated pathogen
Clinical/host-associated pathogen
Pathogen.cl
The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed.
contig N99
The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. A large contig count may indicate insufficient read coverage.
contig count QC threshold
Indicates how the knowledge derived from the project can be applied, and to what field(s).
Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch.
project relevance
agricultural project relevance
medical knowledge relevance
industrial processing relevance
evolution modelling relevance
environmental project relevance
model organism relevance
The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification.
obsolete: NCBI BioProject model
obsolete: NCBI SRA model
Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a BioSample_submission_facilitator field and a BioSample_contact_information field?
Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected.
draft NCBI BioSample model - mixed clinical and environmental/food/other
monoisolate
A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred.
monoisolate sample scope
multiisolate
A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species).
This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated.
multiisolate sample scope
multispecies
A multi-species sample scope involves a sample representing multiple species.
multispecies sample scope
environment
An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies.
environment sample scope
A synthetic sample scope involves a sample synthesized in a laboratory.
synthetic sample scope
single cell
Other project objective: specify an objective not listed above
other project objective
environmental, food or other pathogen
environmental/food/other
Pathogen.env
whole
Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes.
whole genomic data capture
raw sequence reads
A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories
raw sequence read objective
sequence
A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies)
sequence project objective
analysis
An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files.
This defn. could be a negation of the "not otherwise indicated".
analysis objective
assembly
Submission of genome assembly (AGP data)
assembly objective
annotation
Sequence annotation data
sequence annotation objective
sequence variation
Variation: identification of sequence variation data for submission to dbSNP or dbVAR
sequence variation project objective
epigenetic markers
DNA methylation, histone modification, chromatin accessibility datasets
epigenetic markers objective
expression
Expression: assays of transcript or protein existence or abundance
transcript or protein expression objective
maps
Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc.
mapping objective
Phenotypic descriptive data.
phenotypic observation data from specimen
select sequence if any sequence data is generated from this project.
sequencing
sequencing project method
array
Select Array if that is the primary method and no sequence data is submitted
array project method
mass spectrometry
Select Mass Spectrometry if that is the primary method
mass spectrometry project method
order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C42775 # email address GENEPIO:0001756 # phone
contact specification - person
A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains.
investigation datum
An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement.
commensal role
draft isolate details model
A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time.
subject age
draft NCBI component model
draft IRIDA BioSample model
draft GenEpiO epidemiology case record
A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields.
subject description
host description
NCBI BioSample
The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained".
host profile or identifers
A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event.
This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id"
subject identifier
Name of disease in a subject that is related to a given investigation, study and/or specimen.
Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067
subject disease
INSDC term (top level)
A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason.
NCBI Biosample: missing
missing
'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb
A categorical choice recorded when a measurable datum does not apply to a given context.
not applicable
A categorical choice recorded when a datum was not measured with respect to some entity during some process.
NCBI Biosample: not collected
not collected
draft isolate identifier model
draft GenEpiO isolate testing model
draft NCBI isolate source location model
draft GenEpiO isolate environment model
A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event.
subject disease stage
environmental datum
temperature of sample
de-novo assembly
obsolete: sample body source
contig pre-analysis minimum length QC threshold
A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics.
QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter.
contig length QC threshold
The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size.
"Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia
contig NG50
A contig length is the count of base pairs in a given sequence assembly contig.
contig length
Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation.
QUAST manual
contig L50
The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths.
contig LG99
An organism isolate datum is any datum pertaining to an isolate organism
obsolete: specimen from subject datum
A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site
animal body product
This is the scientific role or category that the subject organism or material has with respect to an investigation.
obsolete: specimen source material category
draft GenEpiO general information record
An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens.
antigenic formula
This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.)
specimen organism taxonomy (species)
An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic.
identifier model
help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt
The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...)
curator organization name
An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it.
isolate identifier
An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator.
identifier status
GenEpiO
A data protection role is a role (or user permission) that a user has with respect to particular data.
A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses.
data protection role
An identifier used in the initial submission of content to a repository.
original submission
This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary.
NCBI Contributing organization / project
food - liquid
draft NCBI BioSample identifier model
An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC.
INSDC institution code
draft IRIDA epidemiological case model
An identifier that had been used previously but is no longer promoted.
previous (archaic) identifier
A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location
geographic location datum
A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy.
A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable.
obsolete: categorical tree specification
A geographic coordinate entity composed of both latitude and longitude components.
latitude and longitude coordinate (ISO 6709)
order: NCIT:C25464 # country ENVO:00000005 # state / province etc.
Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"
draft NCBI BioSample geo_loc_name model
draft GenEpiO isolate sequencing model
A case ID is a unique identifier associated with a particular episode of care for an individual or animal.
case identifier
An animal that has had a substantial part of its reproductive organs removed surgically.
Not a PATO phenotypic sex catigorical value.
neuter
'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other.
NCBI BioSample: 'pooled male and female'
pooled male and female
A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated.
undetermined
in process
swimming / wading
NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment.
infection detail datum
This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis.
antibiotics required
The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.
International Nucleotide Database Collaboration standard
INSDC standard
outcome of pregnancy associated with illness
a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage.
not provided
stable health status
induced abortion
live birth
obsolete: gestation duration (weeks)
date of pregnancy outcome
contact specification - physician
obsolete: matrix - solid
contact specification - parent/guardian
contact specification - patient
draft GenEpiO case epidemiology record
order: NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address NCIT:C25621 # postal code
The address component of a contact specification.
contact specification - address
obsolete: draft IRIDA model
A datum related to the sequencing assay process applied to an isolate.
laboratory sequencing datum
host illness associated with
draft subject demographic specification
E. coli K antigen specification
other antigen specification
E. coli serotype specification
Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap.
Salmonella serovar specification
A lab test specification indicates the inputs and outputs (results / conclusions) of a test.
test specification
listeria antigen
obsolete: matrix - fluid
listeria serotype 1/2a
listeria serotype 1/2b
listeria serotype 1/2c
listeria serotype 1/2
listeria serotype 3a
listeria serotype 3b
listeria serotype 4a
listeria serotype 4b
listeria serotype 4c
listeria serotype 4d
listeria serotype 4e
non-monocytogenes listeria antigen
listeria serotype 3c
textual test result
This is an organizational category for grouping parameters relevant to biomedical research projects.
obsolete: draft GenEpiO BioProject standard
NCBI BioSample collection code
draft NCBI BioSample host model
food - solid
lab test datum
Xbal
Ascl
Smal
Blnl
Apal
Kpnl
Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate.
NCBI Biosample
subgroup
help:This is an optional additional subtype classification as per organism convention
A viral subtype is a classification name for a virus according to some protocol.
viral subtype
serotype specification
IRIDA
An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a.
SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002
phage type specification
obsolete: swab - food contact surface
An NCBI culture collection is a composite identifier containing “institution code:collection code”.
Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier.
NCBI culture collection
The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides.
NCBI specimen voucher
culture identifier
human; dog; horse
The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen.
Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided.
subject organism common name
temperature of air - average daily
obsolete: swab - inanimate object surface
obsolete: swab - meat
obsolete: swab - rectal swab
obsolete: swab - tissue
unknown source
patient sample
human clinical specimen
"environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO
obsolete: environmental (swab or sampling)
avian - wild
avian - domesticated
human clinical specimen - invasive
In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution
Wikipedia
Normally falls within the bounds of 0 - 14
pH measurement
precipitation
The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project.
assembly and annotation project objective
line list row record
This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis.
draft GenEpiO component record
region
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
subnational region
A data standard related to public health research and service delivery.
public health data standard
Reagent: material studied was obtained by chemical reaction, precipitation.
reagent derived material from specimen
transcriptome
Transcriptome: transcript and/or expression data.
transcriptome data from specimen
Proteome material is protein or peptide sequences.
proteome data derived from specimen
Purified chromosome: one or more chromosomes or replicons were experimentally purified.
purified chromosome from specimen
targeted locus/loci
TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard).
Targeted Locus Loci data capture
clone ends
CloneEnds: capturing clone end data.
clone end data capture
exome
Exome: capturing exon-specific data.
exome specific data capture
random survey
Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material
Is this with respect to an isolate or a specimen derived culture?
random survey data capture
This is a collection of various human (and animal contact location) contact information specifications used in data standards.
contact specification
order: NCIT:C40978 # phone GENEPIO:0001896 # phone type
contact specification - phone
millimetres per day
obsolete: millisiemens
millisiemens per centimetre
cubic metre per second
micromole per kilogram
micromole per litre
quality control record
Standard draft: describing the minimum information needed for submission to a public database.
1 - standard draft
High quality draft: describing sequences with little to no manual review.
2 - high quality draft
Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present.
3 - improved high quality draft
Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible.
4 - annotation-directed improvement
Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure.
5 - non-contiguous finished
Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome.
6 - finished
The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths.
contig NG99
contig LG50
Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation.
contig L99
A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted.
subject age at time of specimen collection
A public health related data standard involving a particular species of pathogen.
pathogen specific data standard
The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions.
draft tuberculosis contextual data standard
The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format
draft PulseNet Canada Salmonella submission standard
A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme.
PFGE Xbal pattern
A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme.
PFGE Blnl pattern
NLEP ID
An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP)
Pulsenet Canada spreadsheet.
National Laboratory for Enteric Pathogens Identifier
Date an uploaded sample was re-uploaded or had its metadata modified.
upload modified date
A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip.
travel destination
A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal
This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain.
symptom duration
The city where a specimen was collected (taken) from a subject or environment
specimen collection location - city
obsolete: sample city
This is the genus-level taxonomic name of an organism playing a pathogen role
genus of pathogen
This is the species-level taxonomic name of an organism playing a pathogen role
species of pathogen
A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness
symptom cessation date
This is a catch-all category for listing specimen related terms
specimen datum
isolate identifier specification
The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified.
data obfuscated
The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated.
data aggregated
A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted).
limited data set
help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users.
A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them.
Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature.
Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/
de-identified data
A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data.
data protected
A datum containing the name of persons or institute who collected a given specimen.
specimen collector
NCBI BioSample culture identifier
A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary.
user identifier
sequence identifier
metagenomic species identification
Note: REPLACE WITH Citation: SIO_000174 ????
document citation identifier
organization identifier
collection identifier
variant calling / pathogen identification and clustering
isolate (pathogen) identification
obsolete: NCBI BioSample ID -
1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 2) CD8+ T cells from female TSG6-knockout BALB/c mouse 3) Human metagenome isolated from urine of healthy female
A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission.
NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository.
specimen title
draft GenEpiO isolate source context
A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns.
restricted access
State (United States of America)
A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging
health status trend datum
The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.
Integrated Taxonomic Information System
ITIS
MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity.
Medical Subject Headings
MESH
The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.
National Cancer Institude Thesaurus
NCIT
The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction.
NIFSTD
SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International.
SNOMEDCT
ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture.
UN FAO Fisheries and Aquaculture Statistics and Information Branch database
ASFIS
FTT
TGN
Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles.
SWEETRealm
The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
Geonames
EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada.
EcoLexicon
A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology.
draft IRIDA standard
ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest.
ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1.
Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas
American National Standards Institute
ANSI INCITS 38
The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical.
GNISID
LTER
order: OBI:0001628 # investigation identifier OBI:0001616 # specimen identifier GENEPIO:0001808 # specimen title GENEPIO:0000113 # specimen category sep:00196 # specimen description OBI:0001479 # specimen from organism GENEPIO:0001640 # specimen organism taxonomy (species) GENEPIO:0000027 # specimen source context GENEPIO:0001722 # NCBI specimen voucher GENEPIO:0001429 # strain identifier GENEPIO:0001798 # NCBI BioSample culture identifier GENEPIO:0001717 # viral subtype OMP:0000207 # serotype phenotype SO:0001027 # genotype GENEPIO:0001079 # serovar GENEPIO:0001716 # subgroup GENEPIO:0001055 # NCBI pathotype GENEPIO:0001054 # isolate passage history GENEPIO:0001656 # latitude and longitude coordinate GENEPIO:0001657 # NCBI BioSample geo_loc_name model GENEPIO:0001051 # NCBI BioSample isolate (human name or description) GENEPIO:0001648 # NCBI Contributing organization / project GENEPIO:0001797 # specimen collector OBI:0001619 # specimen collection date OBI:0001888 # sequencing facility contact person GENEPIO:0001651 # INSDC institution code GENEPIO:0001721 # NCBI culture collection GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0001724 # subject organism common name GENEPIO:0001775 # subject age at time of specimen collection GENEPIO:0000026 # subject health status at time of specimen extraction GENEPIO:0000031 # subject sex GENEPIO:0001614 # subject description GENEPIO:0001617 # subject disease GENEPIO:0001625 # subject disease stage GENEPIO:0001212 # subject disease outcome
A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays".
NCBI BioSample Pathogen.cl standard
The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/
NCBI BioProject standard
Objective
The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021
Project Accession
Methodology
The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients
American Hospital Association HIPAA Standard
AHA HIPPA standard
PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
NCBI PubMed
PubMed
PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks.
Pulse Net International BioSample Metadata
PulseNet submission standard
AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf
Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent.
AHA Hippa: Good
good health status
Good
satisfactory
Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable.
fair health status
fair
Stable
Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable.
serious health status
Serious
A health status history datum is a record of the longer-term pattern or presence of a given patient's health status.
health status history datum
(0,0) is the origin of the cartesian coordinate system.
"In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry."
origin
United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions.
National Health Service terminology
NHS standard
Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this.
critical but stable health status
critical but stable
NHS Terms: https://en.wikipedia.org/wiki/Medical_state
comfortable health status
Comfortable
progressing well health status
progressing well
Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state.
discharged from hospital
discharged
A data item which is about the collection state of a datum at some point in time.
Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: Unknown/Not Applicable/Censored Allowed Unknown/not applicable/not available/ available upon request
A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made.
datum status
INSDC missing value reporting terms: http://www.ebi.ac.uk/ena/about/missing-values-reporting
A categorical choice indicating that a datum is available for retrieval.
In theory any datum that has a recorded value has 'recorded' for its datum status.
recorded
Patient is awaiting physician and/or assessment.
Very similar to 'datum status' 'in process' status.
undetermined health status - awaiting assessment
deteriorating
worsening health trend
This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates.
A decimal latitude measurement in degrees in conformance with the ISO 6709 standard.
This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: 'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]'
A decimal longitude measurement in degrees in conformance with the ISO 6709 standard.
A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension
A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end.
datetime range intermediate
datetime range item
The ending date of a process
datetime range end
The starting date of a process
datetime range start
A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time.
A Canadian postal code is a postal code that pertains to a geographic region of Canada.
Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account.
A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target.
obsolete: US postal code
entity history record
generic range history record
A set does not have a direct distance metric between its members.
A product name and model number of a manufacturer's genomic (dna) sequencer.
sequencing instrument model
A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant.
circle
Illumina platform
Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)."
Complete Genomics platform
earth area boundary census
Roche LS454 platform
PacBio platform
SOLiD 4hq System
SOLiD 5500
SOLiD 5500xl
SOLiD PI System
SOLiD System 2.0
SOLiD System 3.0
A two dimensional entity is an entity composed of one or more points on a two dimensional surface.
2D entity
454 Genome Sequencer FLX Titanium
454 Genome Sequencer
454 Genome Sequencer Junior
Whether any method was used to select for or against, enrich, or screen the material being sequenced.
library selection
Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
5-methylcytidine antibody method
Cap-analysis gene expression.
CAGE method
Cot-filtered highly repetitive genomic DNA
CF-H method
Cot-filtered moderately repetitive genomic DNA
CF-M method
Cot-filtered single/low-copy genomic DNA
CF-S method
Cot-filtered theoretical single-copy genomic DNA
CF-T method
Chromatin immunoprecipitation
ChIP method
Deoxyribonuclease (MNase) digestion
DNAse method
Hypo-methylated partial restriction digest
HMPR method
Selection by hybridization in array or solution.
Hybrid Selection method
Enrichment by methyl-CpG binding domain.
NCBI SRA: MBD2 protein methyl-CpG binding domain
MBD2 protein methyl-CpG binding domain method
Methyl Filtrated
MF method
Micrococcal Nuclease (MNase) digestion
MNase method
Methylation Spanning Linking Library
MSLL method
Source material was selected by designed primers.
PCR method
Rapid Amplification of cDNA Ends.
RACE method
Source material was selected by randomly generated primers.
RANDOM PCR method
Random selection by shearing or other method.
RANDOM method
Source material was selected by reverse transcription PCR
RT-PCR method
Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
Reduced Representation method
DNA fractionation using restriction enzymes.
Restriction Digest method
PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA.
cDNA method
Physical selection of size appropriate targets.
size fractionation method
Other library enrichment, screening, or selection process.
other library method
The library source specifies the type of source material that is being sequenced.
library source
Genomic DNA (includes PCR products from genomic DNA).
genomic source
Mixed material from metagenome.
metagenomic source
Transcription products from community targets
metatranscriptomic source
Other, unspecified, or unknown library source material.
other library source
Synthetic DNA.
synthetic source
Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
transcriptomic source
Viral RNA.
viral RNA source
Sequencing technique intended for this library.
library strategy
Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA
amplicon strategy
MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status.
Bisulfite-Seq strategy
Clone end (5', 3', or both) sequencing.
clone end strategy
Genomic clone based (hierarchical) sequencing.
clone strategy
Concatenated Tag Sequencing
CTS strategy
Direct sequencing of chromatin immunoprecipitates.
ChIP-Seq strategy
Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.
DNase-Hypersensitivity strategy
Single pass sequencing of cDNA templates
EST strategy
Sequencing intended to finish (close) gaps in existing coverage.
finishing strategy
Full-length sequencing of cDNA templates
FL-cDNA strategy
Direct sequencing of methylated fractions sequencing strategy.
MBD-Seq strategy
Direct sequencing following MNase digestion.
MNase-Seq strategy
Methylation-Sensitive Restriction Enzyme Sequencing strategy.
MRE-Seq strategy
Methylated DNA Immunoprecipitation Sequencing strategy.
MeDIP-Seq strategy
Library strategy not listed.
other library strategy
Shotgun of pooled clones (usually BACs and Fosmids).
pool clone strategy
Random sequencing of whole transcriptome.
RNA-Seq strategy
Random sequencing of a whole chromosome or other replicon isolated from a genome.
WCS strategy
Random sequencing of the whole genome.
WGS strategy
Random sequencing of exonic regions selected from the genome.
WXS strategy
Free form text describing the protocol by which the sequencing library was constructed.
library construction protocol
The submitter's name for this library.
NCBI SRA: LIBRARY_NAME
library name
A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface.
2D boundary
cfu/100mL
A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid.
Should this be deprecated? Need to find working examples that actually use / 100mL.
colony forming unit per 100 milliliter
A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming.
decimal quantity unit
draft tuberculosis - dataset features and provenance
draft tuberculosis - case specimen characteristics
draft tuberculosis - case subject characteristics
draft tuberculosis - case risk factors
draft tuberculosis - case clinical presentation
draft tuberculosis - case laboratory testing
draft tuberculosis - case medication
draft isolate whole genome sequencing model
draft tuberculosis - case model
A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin.
Mycobacterium tuberculosis lineage
A TB-Lineage identification tool using spoligotypes and MIRU data: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html
TB lineage 2 - East-Asian, includes Bejing
TB lineage 3 - East-African Indian, includes CAS/Delhi
TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv
TB lineage 1 - Indo-Oceanic
TB lineage 5 - West African 1
TB lineage 6 - West African 2
An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens.
isolate preparation facility
plant product
geospatial name
A personal health datum is a datum that pertains to the health situation or history of an individual.
Personal health datum covers the following information 'has member' some 'analytic datum' 'has member' some 'behavioural risk factor' 'has member' some 'country of birth' 'has member' some 'dietary restrictions' 'has member' some 'Disease Attributes' 'has member' some 'health status history datum' 'has member' some 'health status trend datum' 'has member' some 'host hospital service status' 'has member' some 'subject disease stage' 'has member' some 'subject health status' 'has member' some 'subject health status (AHA)' 'has member' some 'subject health status (GSCID-BRC)' 'has member' some 'subject health status (NCIT)' 'has member' some 'subject health status (UK NHS)' 'has member' some 'subject health status at time of specimen extraction' 'has member' some 'tuberculosis disease anatomical site' 'has member' some comorbidity 'has member' some disease 'has member' some symptom
personal health datum
A host hospital service status indicates the state of a host's interaction with hospital medical services.
host hospital service status
admitted to hospital
Received treatment but not admitted.
treated and released (not admitted to hospital)
Treated and Released
Received treatment. Transferred to a different facility.
treated and transferred
Treated and Transferred
satisfactory health status
subject health status (UK NHS)
subject health status (AHA)
stable health trend
An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them.
obsolete: ordinal variable
mapping (reference based)
data protection item
subject provided consent
An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings.
ordinal value specification
consent datum
agency provided consent
draft ISO sequence repository field
Centre of circle, ellipse or parabola; centre of mass.
A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point.
Probably a better formal math defn?
centre point
This covers the following entities: 'has member' some 'antimicrobial phenotype' 'has member' some 'antimicrobial resistance test drug' 'has member' some 'antimicrobial resistance test platform' 'has member' some 'antimicrobial resistance testing method' 'has member' some 'antimicrobial resistance testing method version or reagent' 'has member' some 'antimicrobial resistance testing reference standard' 'has member' some 'antimicrobial resistance testing reference standard version' 'has member' some 'antimicrobial resistance tissue specificity' 'has member' some 'antimicrobial resistant plasmid type' 'has member' some 'automated testing platform vendor' 'has member' some 'draft antibiogram drug test model' 'has member' some 'in-vitro microbial susceptibility test' 'has member' some 'measurement comparator' 'has member' some 'MIC unit' 'has member' some 'MIC value' 'has member' some 'Minimum Inhibitory Concentration Test' 'has member' some 'test drug maximum concentration' 'has member' some 'test drug minimum concentration' 'has member' some 'tuberculosis treatment drug'
This is a collection of antibiotic resistance process parameters and outputs
phenotypic antimicrobial drug susceptibility test datum
The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT)
obsolete: antimicrobial resistance phenotype
Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic.
obsolete: antibiotic intermediate resistance (I)
Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic.
obsolete: antibiotic nonsensitive (high resistance)
A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive.
Damion Dooley note: Is this the same as "indeterminate"?
antibiotic resistance not defined
Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic.
obsolete: antibiotic resistant (R)
Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic.
obsolete: antibiotic sensitive (S)
Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given.
obsolete: sensitive - dose dependent
A MIC test measurement resulting from a laboratory dilution method.
Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific.
MIC dilution measurement datum
The type of assay used to determine the minimum inhibitory concentration.
obsolete: antimicrobial resistance testing method
obsolete: agar dilution evidence
The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used.
antimicrobial resistance testing method device or reagent
antimicrobial resistant plasmid type
The instrumentation used to determine minimum inhibitory concentration values.
obsolete: antimicrobial resistance testing platform
obsolete: Microscan
obsolete: Phoenix
obsolete: Sensititre
obsolete: Vitek
obsolete: Trek
obsolete: manual - noncommercial
The manufacturer of an antibiotic resistance lab typing platform
obsolete: antimicrobial resistance testing platform vendor
obsolete: Siemens
obsolete: Biomérieux
obsolete: Becton Dickinson
A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial.
E-Test
Epsilometer test
Etest (device)
GM-NEG
The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes.
obsolete: antimicrobial resistance testing reference standard
BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership
obsolete: British Society for Antimicrobial Chemotherapy (BSAC)
The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards
obsolete: Clinical and Laboratory Standards Institute (CLSI)
DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations.
Deutsches Institut für Normung
obsolete: German Institute for Standardization (DIN)
EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing.
obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST)
obsolete: National Committee on Clinical Laboratory Standards (NCCLS)
La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites.
The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents.
This isn't at moment considered a valid EBI antibiogram choice?
obsolete: Société Française de Microbiologie (SFM)
Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD).
obsolete: SIR
obsolete: WRG
first line tuberculosis drug
last resort antibiotic
NIAID standard
NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases.
National Institute of Allergy and Infectious Disease standard
A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers.
RefSeq accession identifier
A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison.
Genomic Standards Consortium (GSC) standard
A landform, biome or built environment at site that a given specimen was collected from.
specimen collection site - geographic feature
A particular human patient, or a given animal or plant.
An investigative subject which is an organism.
subject organism
help=The number of passages should be expressed as a numerical value.
The number of serial iterations that an isolate is grown in one environment.
number of passages
help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation.
A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment.
passage protocol
The unit provided for an antibiotic drug test dosage.
obsolete: drug minimum inhibitory concentration unit
order: GENEPIO:0001237 # specimen type (host or environmental context) OBI:0001619 # specimen collection date OBI:0000659 # specimen collection process GENEPIO:0002094 # specimen collection device GENEPIO:00001600 # draft sequence repository data - geographic location ENVO:00010483 # environmental material ENVO:00002297 # environmental feature GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0000110 # subject health status GENEPIO:0001617 # subject disease GENEPIO:0000028 # subject body product GENEPIO:0000025 # specimen source anatomical site FOODON:03411564 # draft sequence repository data - food processing
draft sequence repository data - specimen collection
order: GENEPIO:0002105 # Specimen processing organization role NCIT:C93874 # organization name NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address
Contact information for an organization related to specimen collection, processing or storage.
contact specification - specimen related organization
order: GENEPIO:0002082 # specimen related organization GENEPIO:0002081 # specimen collection GENEPIO:0002086 # geographic location GENEPIO:0002084 # isolate GENEPIO:0002087 # isolate history GENEPIO:0002106 # food specimen GENEPIO:0002088 # antibiogram GENEPIO:0002085 # sequencing GENEPIO:0002090 # sequencing QC GENEPIO:0002089 # virulence GENEPIO:0002092 # submission to EBI GENEPIO:0002091 # submission to NCBI/DDBJ
This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology.
draft sequence repository contextual data standard
order: GENEPIO:0001640 # specimen taxonomy GENEPIO:0001429 # strain identifier GENEPIO:0001644 # isolate identifier OBI:0000079 # culture medium GENEPIO:0002107 # isolation medium
draft sequence repository data - isolate
order: GENEPIO:0000069 # sequencing date OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). GENEPIO:0002093 # sequencing dna extraction method EFO:0000683 # replicate GENEPIO:0000085 # library preparation kit GENEPIO:0000149 # library preparation kit version GENEPIO:0000075 # sequencing chemistry GENEPIO:0001921 # sequencing instrument model GENEPIO:0000150 # read trimming and filtering software GENEPIO:0000084 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000090 # assembly method GENEPIO:0000151 # bioinformatics pipeline name GENEPIO:0000153 # bioinformatics pipeline protocol GENEPIO:0000152 # bioinformatics pipeline version GENEPIO:0000095 # genome annotation algorithm
draft sequence repository data - sequencing
order: GENEPIO_0001656 # latitude and longitude ISO 6709 GENEPIO:0000118 # specimen collection country GENEPIO:0002097 # specimen collection state/prov/ter/region GENEPIO:0001785 # specimen collection city
The geographical origin of the sample by city, region, country or latitude and logitude.
draft sequence repository data - geographic location
order: GENEPIO:0002078 # number of passages GENEPIO:0002079 # passage protocol
draft sequence repository data - isolate passage history
order: GENEPIO:0001100 # antimicrobial drug tests GENEPIO:0002101 # test drug minimum concentration GENEPIO:0002100 # test drug maximum concentration GENEPIO:0002045 # antimicrobial resistance testing method GENEPIO:0002047 # antimicrobial testing method version or reagent GENEPIO:0002062 # antimicrobial resistance testing reference standard GENEPIO:0002049 # antimicrobial resistance testing platform
A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested.
draft sequence repository data - antibiogram
order: GENEPIO:0002130 # Virulence factor name GENEPIO:0002131 # Virulence testing protocol GENEPIO:0002132 # detection limit
The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins.
draft sequence repository data - virulence
order: OBI:0001941 # N50 GENEPIO_0000092 # sequencing depth / read coverage
Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific.
draft sequence repository data - sequencing quality control
order: OBI:0001616 # specimen identifier GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0001657 # geo_loc_name GENEPIO:0001656 # latitude and longitude coord GENEPIO:0000027 # specimen source context GENEPIO:0001567 # subject organism taxonomy GENEPIO:0001724 # subject organism common name GENEPIO:0001617 # subject disease
draft sequence repository data - submission to NCBI/DDBJ
order: GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0001079 # serovar GENEPIO:0002135 # EBI environmental feature GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0002086 # geographic location GENEPIO:0000027 # specimen source context GENEPIO:0002076 # geographic feature GENEPIO:0001567 # subject taxonomy GENEPIO:0000110 # subject health status
draft sequence repository data - submission to EBI
The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means.
sequencing dna extraction method datum
Moved term to OBI, deprecated in favour of the OBI version.
obsolete: specimen collection device
The name and version of the software used to merge paired-end reads before assembly.
read paired-end merging software
The name and version of the software product used for removal of adapter sequences from demultiplexed data reads
read adapter trimming software
An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event.
specimen collection location - state/province/territory/region
A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are present to the antimicrobial in question.
obsolete: wild type (WT)
A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent.
obsolete: non-wild type (NWT)
This is the maximum concentration of a drug applied during an an assay.
test drug maximum concentration
This is the minimum concentration of a drug applied during an an assay.
test drug minimum concentration
The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results.
obsolete: antimicrobial resistance tissue specificity
order: NCIT:C115935 # healthy NCIT:C126054 # non-pathalogical NCIT:C25610 # pathologic NCIT:C82508 # life threatening NCIT:C28554 # deceased
subject health status (NCIT)
order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone
contact specification - professional role
An organization related to the collection, isolate production, sequencing or storage of specimen material or data.
specimen processing organization type
order: GENEPIO:0001533 # food specimen type FOODON:03450002 # food cooking method FOODON:03440011 # extent of heat treatment FOODON:03430113 # physical state, shape or form FOODON:03470107 # food preservation method FOODON:03490100 # container or wrapping FOODON:03480020 # food packing medium FOODON:03500010 # food contact surface GENEPIO:0000139 # food cultural origin FOODON:03460111 # treatment applied to food
This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen.
draft sequence repository data - food specimen
An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment.
Chris has proposed this term for OBI as "enrichment culture medium"
isolation medium
order: GENEPIO:0000121 # start date GENEPIO:0000122 # end date GENEPIO:0001783 # travel destination GENEPIO:0001064 # travel mode GENEPIO:0001065 # travel reason
This record details a person's travel movement and duration for epidemiological analysis.
draft travel log specification
order: OBI:0001616 # BioSample_ID GENEPIO:0001640 # Species GENEPIO:0001187 # Antibiotic_Name GENEPIO:0002062 # AST_Standard GENEPIO:0002111 # Breakpoint_version NCIT:C85540 # Laboratory_typing_method GENEPIO:0002112 # Measurement GENEPIO:0002080 # Measurement_units GENEPIO:0001001 # Measurement_sign NCIT:C85539 # Resistance_phenotype GENEPIO:0002181 # Resistance_phenotype - ECOFF GENEPIO:0002049 # Platform
A standard for European Bioinformatics Institute (EBI) antibiogram data submission
draft EBI antimicrobial susceptibility test V. 2017-08-30
A MIC test measurement resulting from a laboratory diffusion method.
Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method".
MIC diffusion measurement datum
The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate.
antimicrobial resistance testing reference standard version
This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units.
draft sequence repository data - antibiogram MIC measurement
time value specification
The process of collecting a portion of feces from an organism.
Emma Griffiths
stool collection
feces collection
The process of collecting a portion of urine from an organism.
sputum collection
The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.
rinsing for specimen collection
The process of collecting specimen material using a swab collection device.
swabbing for specimen collection
The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury.
exudate collection
The removal or collection of specimen material through the use of suction.
vacuuming for specimen collection
NOTE: there are different types of tubes with coloured caps indicating different preservatives etc.
tube containing media or preservative
tube containing antimicrobial
A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures.
Whirlpak sampling bag
spoon
fork
A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion.
hand scoop
trier
A device which generates a vacuum to provide suction of material.
vaccum device
investigation identifier specification
order: GENEPIO:0001640 # taxonomy GENEPIO:0002086 # geographic location GENEPIO:0002076 # geographic feature GENEPIO:0002106 # food FOODON:03510136 # food consumer GENEPIO:0002094 # specimen collection device GENEPIO:0000025 # anatomical site GENEPIO:0000028 # body product GENEPIO:0001724 # host organism common name GENEPIO:0001567 # host taxonomy UBERON:0000105 # life cycle GENEPIO:0001639 # antigenic formula GENEPIO:0001718 # serotype specification GENEPIO:0000045 # PFGE test specification
This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records.
draft Enterobase contextual data standard
The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive.
virulence factor name
help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models.
The laboratory protocol used to determine virulence phenotypes and markers.
virulence testing protocol name
help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs.
The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure.
detection limit
A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography.
disease cluster
A disease cluster in which two or more cases have been linked by an infectious disease transmission process.
infectious disease cluster
help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier
Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture).
ENA Webin:environmental_feature
EBI ENA Webin environmental feature
The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions.
EBI European Nucleotide Archive Webin
help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X).
Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5).
A data item which is the amount of a reference sequence covered by a sequence of interest.
breadth of coverage
The mean contig length is the count of base pairs in the average size contig of the sequence assembly.
mean contig length
order: GENEPIO:0000084 # read adapter trimming (y/n) GENEPIO:0002096 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000150 # read trimming and filtering software
The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads.
raw sequence data processing datum
Name of strain from which sample was obtained OR name of isolate from which sample was obtained.
specimen strain or isolate identifier
The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W
latitude and longitude coordinate (NCBI BioSample format)
decimal value specification
floating point value specification
unsigned integer
A 32 bit number having a range 0 - 4294967295.
unsigned integer value specification
date value specification
A specification for the size of an assembled genome as measured in base pairs.
This is a decimal because the megabasepair unit may involve a fractional component.
assembly genome size specification
sequencing facility name specification
date (ISO 8601)
A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime
date value specification (ISO 8601)
strain identifier specification
MIC diffusion measurement specification
unsigned short
A 16 bit integer ranging from 0 - 65535
unsigned short integer value specification
genomic sequence length specification
MIC dilution measurement specification
The date on which a specimen was collected, in ISO 8601 format.
specimen collection date (ISO 8601)
date of diagnosis (ISO 8601)
subject age specification
subject age at time of specimen collection specification
boolean
A boolean value specification indicates a presence (true value) or absence (false value) of a given feature.
boolean value specification
specimen identifier specification
email address specification
region, province, state or territory specification
A specification for a geographic location that a specimen was collected at.
specimen collection site specification
subject organism common name specification
A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field.
subject identifier specification
subject disease specification
unsigned long integer
A 64 bit integer ranging from 0 - 18446744073709551615
unsigned long integer value specification
The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc.
specimen collection site
drug MIC unit specification
A datum specification for the maximum concentration of a drug applied during an an assay.
test drug maximum concentration specification
test drug minimum concentration specification
listeria antigen specification
URL specification
travel destination specification
specimen source substance specification
Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy".
specimen from organism specification
duration specification
A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference).
obsolete: field specification
obsolete: antimicrobial resistance phenotype - epidemiological cut-off values
PulseNet Canada field
PulseNet Canada Salmonella field
specimen collection service
bioinformatics analysis service
An isolate preparation service prepares isolates for molecular sequencing.
isolate preparation service
order: GENEPIO:0002222 # specimen collection service GENEPIO:0002226 # specimen repository/biobank service GENEPIO:0002224 # isolate preparation service OBI:0001904 # sequencing service OBI:0000992 # DNA sequencing service GENEPIO:0002223 # bioinformatics analysis service
specimen related service
specimen repository/biobank service
Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable.
grave
critical health status
critical
A datum indicating one of six defined subspecies of Salmonella.
Salmonella subspecies
A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme.
PFGE Spel pattern
A collection of organisms that is indicative of faecal contamination.
Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present
fecal indicator
An isolate derived from a food sample.
food isolate
A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes.
microbial 16S RNA typing
E. coli H antigen specification
E. coli O antigen specification
string
string value specification
A sequencing platform brand provided by Helicos corporation (now defunct).
Helicos platform
A sequencing platform provided by the Ion Torrent company.
Ion Torrent platform
A sequencing platform provided by Life Technologies Corporation
Sequencing by Oligonucleotide Ligation and Detection
SOLiD sequening platform
obsolete: drag swab
Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid.
rinse
Animal rinse is a rinse derived from animal material of one or more animals.
animal rinse
obsolete: surface wipe
A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium.
A fluid that is obtained from rinsing meat for the purpose of collecting materials and organisms that are on its surface.
A sequencing platform provided by the BGI Genomics company.
A sequencing platform provided by the MGI company.
A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted.
Emma J Griffiths
A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.
Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term.
An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.
A personal health datum which specifies host health complications at time of specimen collection.
host health complications at time of specimen collection
A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection.
pre-existing conditions and risk factors at time of specimen collection
A personal health datum which specifies host signs and symptoms at time of specimen collection.
signs and symptoms at time of specimen collection
A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work.
environmental testing sampling strategy
A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research.
clinical trial sampling strategy
A collection of contextual data attributes pertaining to a pathogen in an environmental sample, as specified by the International Nucleotide Sequence Database Collaboration (INSDC).
Environmental Pathogen Attribute Package (Pathogen.env)
A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes.
survey study sampling strategy
The "specimen collector sample ID" is where one can store sample identifiers given by the specimen collector.
A data item which is a location for a predetermined type of data.
data slot
data field
This "or" class is just to represent an equivalency with a commonly used classification, it should not have subclasses under it. (2022-12-22)
State or Province or Territory
symptom
position of phenotype abnormality
Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards
Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code.
pregnant woman
data source
Database that originally provided the interaction record for exchange purposes.
Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields.
source database
tissue collection (necropsy)
A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed]
necropsy
The Archaea constitute a domain and kingdom of single-celled microorganisms
subspecies
Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity
healthy
NCIT offers this alternate definition which GenEpiO intends: "A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited."
Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user
A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material.
diseased
sick
deceased
phone
A hollow cylinder, especially one for holding or conveying liquids.
Damion Dooley's note: It can also be used as an authorization token in some identification processes.
Damion Dooley's note: here "sample" means more than one specimen merged together.
pooled
brand name
An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI]
NCIT Thesaurus
investigative subject
antimicrobial resistance testing method
E-test (Epsilometry)
organization name
NCI Thesaurus
antibiotic treatment
fetal death (miscarriage/still birth)
Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in'
Project Description
sample identifier
specimen collection date
help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location.
Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises.
See http://www.csgnetwork.com/gpscoordconv.html See http://www.geomidpoint.com/latlon.html See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 See http://www.w3.org/2003/01/geo/wgs84_pos
Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. " 'country name' inheres in some 'sovereign state/country'". Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs "Republic of China"). Both point to needing a single entity with multiple names.
target material
Used in NCBI BioProject specifcation
specimen sample scope
sequencing facility
project objective
project method
specimen provider PI email
categorical
scalar
Damion Dooley's note: Often a value specification may need to allow for a "data item state" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state.
sample
diagnosis
An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
extended organism
complications
A type of Shiga toxin found in E. coli
Shiga toxin 1
A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1
Shiga toxin 2
MLST typing
A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
physician role
Damion's Note: Future use might prefer: CMO_0000015 body temperature.
NCBI BioSample: female
Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior.
Note that NCBI Biosample has these values allowed: male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected
NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/
Damion Dooley's note: We can't say radius is a subclass of "linear coordinate" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. "length" as quality unfortunately can't pertain to abstract entities, only "real" ones.
social gathering
sequence assembly
http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data'
Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict.
Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for.
Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully!
variable type
A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host.
transmission of infection
Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.
direct transmission
Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles.
indirect transmission
Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth.
congenital
contact transmission
Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen.
contact
Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking.
droplet spread
Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products.
vehicle-born ingestion
organism body product
poultry fluff
Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed.
Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: [1] R. Hodgson and P. J. Keller, "QUDT-quantities, units, dimensions and data types in OWL and XML." Online (September 2011) http://www. qudt.org [2] M. van Assem, H. Rijgersberg, and J. Top, "Ontology of units of measure and related concepts." Semantic Web 4, no. 1 (2013): 3-13. [3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, "The Units Ontology: a tool for integrating units of measurement in science." Database2012 (2012): bas033.
ongoing pregnancy
ancestral group
A personal health datum which specifies host role at time of specimen collection.
host role at time of specimen collection
MLVA typing
Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height.
In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit.
PulseNet: Key
medical health record (history / timeline)
Bacterial bacteriophage typing
obsolete: ancestral group
A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
Welcome to the GenEpiO ontology! The "information content entity" class has many GenEpiO terms. "data item > measurement data item" has many datum terms; see "data representational model" for collections of terms set up for compatibility with 3rd party sources. Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use.
Base class for definitions.
A named element in the model.
Usage example and description.
An attributed label.
A permissible value, accompanied by intended text and an optional mapping to a concept URI.
A collection of subset, type, slot and class definitions.
The definition of a property or a slot.
Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software.
United Nations
MSH
NCI_Thesaurus
home
_test_individual
LabID assigned by NLEP
Country where isolate was collected
SourceCountry
Currently not used for PulseNet Canada
(Province for PNC) where isolate was collected.
Site of the source type where isolate was collected, e.g. blood, CSF, etc.
The source type of the isolate, e.g. human, environmental, etc.
Other countries where the patient traveled
Further description of the source type, e.g. bovine, chicken
Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE
(Province for PNC) additional number used to identify the isolate
Age of patient when isolate was collected
Sex of patient when isolate was collected
Date of collection
Date the isolate is uploaded to the national database after initial upload
Antigenic Formula
Subspecies, I - VI (roman numerals)
O polysaccharide (LPS) Group
Serotype of isolate
Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#)
Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP)
Enzyme name present if part of that national list.
Phage type
Provides LabID, gel and lane information
Status of the isolate; this is only confirmed once CDC runs it.
checked if the isolate is part of NARMS.
Checked if the isolate is part of FoodNet.
XbaI gel where the isolate is located, lane of gel
XbaI pattern assigned by CDC (format XXXXXX.####)
The date the XbaI gel is run
Once the XbaI pattern is named, the status is confirmed by CDC
BlnI gel where the isolate is located, lane of gel
BlnI pattern assigned by CDC (format XXXXXX.####).
The date the BlnI gel is run
Once the BlnI pattern is named, the status is confirmed by CDC
SpeI gel where the isolate is located, lane of gel.
SpeI pattern assigned by CDC (format XXXXXX.####).
The date the SpeI gel is run.
Once the SpeI pattern is named, the status is confirmed by CDC.
Date WHICH (PH?) lab received isolate.
ISO_23418.organization_contact.service
Date the isolate uploaded to the national database.
A Canadian public research university in the province of Manitoba.
The Public Health Agency of Canada is an agency of the Government of Canada that is responsible for public health, emergency preparedness and response, and infectious and chronic disease control and prevention.
PHAC
The Canadian Food Inspection Agency is a regulatory agency that is dedicated to the safeguarding of food, plants, and animals in Canada
CFIA
Agriculture and Agri-Food Canada is the department of the Government of Canada responsible for the federal regulation of agriculture, including policies governing the production, processing, and marketing of all farm, food, and agri-based products.
AAFC
Health Canada is the department of the Government of Canada responsible for national health policy.
Environment and Climate Change Canada, is the department of the Government of Canada, that is responsible for coordinating environmental policies and programs, as well as preserving and enhancing the natural environment and renewable resources. It is also colloquially known by its former name, Environment Canada.
ECCC
Environment Canada
Environment and Climate Change Canada (ECCC)
Fisheries and Oceans Canada, is a department of the Government of Canada that is responsible for developing and implementing policies and programs in support of Canada's economic, ecological and scientific interests in oceans and inland waters.
DFO
intermediate
resistant
susceptible
sensitive
nonsusceptible
nonsensitive
susceptible - dose dependent
SSD
sensitive - dose dependent
Damion Dooley's note: this BFO class is incompatible with "immaterial entity" "n-dimensional concept".
food role
constructed feature
irrigation pond
stool
straw bedding
chicken cage
asian tiger shrimp
black tiger shrimp
gathered
wild
This is a catch-all category for Gazetteer items that have "located in" relations but not an imported GAZETTEER class parent in GenEpiO.
obsolete: has primitive data type
Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity"
This seems to be covered by 'datetime range intermediate'
A datetime set item is a datetime that has been grouped semantically under a given type of process
mobile
work
An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements.
clam, squid, octopus
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
specimen provider PI organization
disease (OGMS)
This value is not present in NCBI BioSample host sex.
derives into
starts during
happens during
starts with
ends with
input of
n-dimensional coordinate system
Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? Linear offset can be decimal or integer or complex, or a count. - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit Angular offset can be radians or degrees.
rectal
cerebrospinal fluid (CSF)