fields_def.txt

#
# Search and output field tag definition
#
# Version 1.7 - pam, 13.02.2024
#
# Fields must be declared in the following order:
#
# TG: Once.         Tag.         Field identifier to be used in an API request in the value of parameter field or query
# DE: Once or more. Description. Describes the content of the field, Used in Help page for API users.
# SH: None or once. Short tag.   Alternate value to be used in an API request in the value of parameter field or query
# PR: Once or more. Prefix.      Prefix in cellosaurus line of txt version selected by short or long tag
# XP: Once or more. Xpath expr.  XML path in cellosaurus XML version selected by short or long tag
# //: Once.         Terminator
#

TG   id
DE   Recommended name. Most frequently the name of the cell line as provided in the original publication.
PR   ID
XP   /cell-line/name-list/name[@type="identifier"]
CC   I know its an exception: that I call it name when it is called ID/identifier
//
TG   sy
DE   List of synonyms. We try to list all the different synonyms for the cell line, including alternative use
DE   of lower and upper cases characters. Misspellings are not included in synonyms (see the "misspelling" tag).   
PR   SY
XP   /cell-line/name-list/name[@type="synonym"]
//
TG   idsy
DE   Recommended name with all its synonyms. Concatenation of ID and SY.
PR   ID
PR   SY
XP   /cell-line/name-list/name
//
TG   ac
DE   Primary accession. It is the unique identifier of the cell line.
DE   It is normally stable across Cellosaurus versions but when two entries are merged, one of the two
DE   accessions stays primary while the second one becomes secondary (see ACAS)  
PR   AC
XP   /cell-line/accession-list/accession[@type="primary"]
//
TG   acas
DE   Primary and secondary accession. Secondary accession are former primary accession kept here to ensure the access to a cell
DE   line via old identifiers.
PR   AC
PR   AS
XP   /cell-line/accession-list/accession
CC   No need to allow separate query/retrieval of primary and secondary AC
CC   Pam: ok but useful for solr and technical reasons
CC   Pam note: we cannot use 'AS' as a solr filed name
//
TG   dr
DE   Cross-references to external resources: cell lines catalogs, databases, 
DE   resources listing cell lines as samples or to ontologies. A cross-reference has two parts: 
DE   the short name of the resource (i.e. CCLE) and an identifier used to locate a particular
DE   entry of the resource related to the cell line. 
DE   For a formal description of all the resources referred to in the Cellosaurus, 
DE   see <a target="_blank" href="https://ftp.expasy.org/databases/cellosaurus/cellosaurus_xrefs.txt">here</href> .
PR   DR
XP   /cell-line/xref-list/xref
CC   No need to have distinct fields for the different resources:
CC   there are too many and there are too many changes from release to release
//
TG   ref
DE   Publication references. Mostly publications describing the establishment of a cell line or its characterization.
DE   Can be journal articles, book chapters, patents and theses. Contains the cross-reference of the publication, 
DE   its title, authors (or group/consortium) and citation elements.
PR   RX
PR   RA
PR   RG
PR   RT
PR   RL
XP   /cell-line/reference-list/reference
XP   /publication
CC   Pam: everything about publications and cell-line internal-id referencing them
//
TG   rx
DE   Publication cross-reference. A unique identifier allowing to access the publication online.
DE   The cross-reference has two parts: the shortname of the online resource (i.e. PubMed, DOI,
DE   PMCID, CLPUB or Patent) and an identifier used to locate the particular publication related 
DE   to the cell line. For a formal description of all the resources referred to in the Cellosaurus,
DE   see <a target="_blank" href="https://ftp.expasy.org/databases/cellosaurus/cellosaurus_xrefs.txt">here</href> .
PR   RX
XP   /cell-line/reference-list/reference
XP   /publication/attribute::internal-id
XP   /publication/xref-list/xref
CC   Pam: publication xrefs with cell-line internal-id referencing them
//
TG   ra
DE   Publication authors. List of authors of a publication referenced in a cell line entry.
PR   RA
PR   RG
XP   /cell-line/reference-list/reference
XP   /publication/attribute::internal-id
XP   /publication/author-list/person
XP   /publication/author-list/consortium
//
TG   rt
DE   Publication title. Title of a publication referenced in a cell line entry.
PR   RT
XP   /cell-line/reference-list/reference
XP   /publication/attribute::internal-id
XP   /publication/title
CC   Note: only a few references with a RG line instead of RA (8 so far).
CC   Alain has put the name of the consortium inside the author-list (ok) as
CC   a "<person name" (example: <person name="The HD iPSC consortium"/>).
CC   Not very elegant but no need to change. Only question do we change the short
CC   tag from "RA" to "RARG" which is not very elegant but would be more correct
CC   in term of content
//
TG   rl
DE   Publication citation elements. Citation elements of a publication referenced in a cell line entry.
PR   RL
XP   /cell-line/reference-list/reference
XP   /publication/attribute::type
XP   /publication/attribute::date
XP   /publication/attribute::journal-name
XP   /publication/attribute::book-title
XP   /publication/attribute::conference-title
XP   /publication/attribute::document-title
XP   /publication/attribute::document-serie-title
XP   /publication/attribute::issn-13
XP   /publication/attribute::volume
XP   /publication/attribute::last-page
XP   /publication/attribute::first-page
XP   /publication/attribute::publisher
XP   /publication/attribute::city
XP   /publication/attribute::institution
XP   /publication/attribute::country
XP   /publication/attribute::internal-id
//
TG   ww
DE   Web page related to the cell line
PR   WW
XP   /cell-line/web-page-list/web-page
//
TG   genome-ancestry
DE   Estimated ethnic ancestry of the donor of a human cell line based on the analysis of its genome.
SH   anc
PR   CC   Genome ancestry
XP   /cell-line/genome-ancestry
//
TG   hla
DE   HLA typing information. Alleles identified on the MHC type I and type II genes of the donor of a human cell line. 
PR   CC   HLA typing
XP   /cell-line/hla-typing-list/hla-typing
CC   For both the API and the full text search: no need to go deep in the structure of the HLA information:
CC   if one really want to get cell lines with a specific HLA allele value for a particular gene lets do that in SPARQL
//
TG   registration
DE   Official list, or register in which the cell line is registered.
SH   reg
PR   CC   Registration
XP   /cell-line/registration-list/registration
//
TG   sequence-variation
DE   Important sequence variations of the cell line compared to the reference genome of the species.
SH   var
PR   CC   Sequence variation
XP   /cell-line/sequence-variation-list/sequence-variation
//
TG   anecdotal
DE   Anecdotal details regarding the cell line (its origin, its name or any other particularity).
SH   anec
PR   CC   Anecdotal
XP   /cell-line/comment-list/comment[@category="Anecdotal"]
//
TG   biotechnology
DE   Type of use of the cell line in a biotechnological context.
SH   biot
PR   CC   Biotechnology
XP   /cell-line/comment-list/comment[@category="Biotechnology"]
//
TG   breed
DE   Breed or subspecies an animal cell line is derived from with breed identifiers from FlyBase_Strain, RS and VBO.
PR   CC   Breed/subspecies
XP   /cell-line/breed
CC   Pam: problem with slash in attribute name "Breed/subspecies", workaround by using starts-with() in XP
//
TG   caution
DE   Errors, inconsistencies, ambiguities regarding the origin or other aspects of the cell line.
PR   CC   Caution
XP   /cell-line/comment-list/comment[@category="Caution"]
//
TG   cell-type
DE   Cell type from which the cell line is derived.
SH   cell
PR   CC   Cell type
XP   /cell-line/cell-type
//
TG   characteristics
DE   Production process or specific biological properties of the cell line.
SH   char
PR   CC   Characteristics
XP   /cell-line/comment-list/comment[@category="Characteristics"]
//
TG   donor-info
DE   Miscellaneous information relevant to the donor of the cell line.
SH   donor
PR   CC   Donor information
XP   /cell-line/comment-list/comment[@category="Donor information"]
CC   Added october 2022
//
TG   derived-from-site
DE   Body part (tissue or organ) the cell line is derived from.
SH   site
PR   CC   Derived from site
XP   /cell-line/derived-from-site-list/derived-from-site
//
TG   discontinued
DE   Discontinuation status of the cell line in a cell line catalog.
SH   disc
PR   CC   Discontinued
XP   /cell-line/comment-list/comment[@category="Discontinued"]
XP   /cell-line/xref-list/xref/discontinued/..
//
TG   doubling-time
DE   Population doubling-time of the cell line.
SH   time
PR   CC   Doubling time
XP   /cell-line/doubling-time-list/doubling-time
CC   For the short tag: I hesitated: if I put CC-DT, it looks like if its concern the "DT" (Date) line. And If put CC-PDT (for population doubling time), a often used abbreviation, it seems weird not to use it inside the Cellosaurus
//
TG   from
DE   Laboratory, research institute, university having established the cell line.
PR   CC   From
XP   /cell-line/comment-list/comment[@category="From"]
//
TG   group
DE   Specific group the cell line belongs to (example: fish cell lines, vaccine production cell lines).
PR   CC   Group
XP   /cell-line/comment-list/comment[@category="Group"]
//
TG   karyotype
DE   Information relevant to the chromosomes of a cell line (often to describe chromosomal abnormalities).
SH   kar
PR   CC   Karyotypic information
XP   /cell-line/comment-list/comment[@category="Karyotypic information"]
//
TG   knockout
DE   Gene(s) knocked-out in the cell line and method to obtain the KO.
SH   ko
PR   CC   Knockout cell
XP   /cell-line/knockout-cell-list/knockout-cell
//
TG   msi
DE   Microsatellite instability degree.
PR   CC   Microsatellite instability
XP   /cell-line/microsatellite-instability-list/microsatellite-instability
//
TG   miscellaneous
DE   Miscellaneous remarks about the cell line.
SH   misc
PR   CC   Miscellaneous
XP   /cell-line/comment-list/comment[@category="Miscellaneous"]
//
TG   misspelling
DE   Identified misspelling(s) of the cell line name with in some case the specific publication or external resource entry where it appears.
SH   miss
PR   CC   Misspelling
XP   /cell-line/misspelling-list/misspelling
//
TG   mab-isotype
DE   Monoclonal antibody isotype. Examples: IgG2a, kappa; IgM, lambda.
SH   mabi
PR   CC   Monoclonal antibody isotype
XP   /cell-line/monoclonal-antibody-isotype-list/monoclonal-antibody-isotype
//
TG   mab-target
DE   Monoclonal antibody target molecule. Generally a specific protein or chemical compound.
SH   mabt
PR   CC   Monoclonal antibody target
XP   /cell-line/monoclonal-antibody-target-list/monoclonal-antibody-target
//
TG   omics
DE   "Omics" study(ies) carried out on the cell line.
PR   CC   Omics
XP   /cell-line/comment-list/comment[@category="Omics"]
//
TG   part-of
DE   The cell line belongs to a specific panel or collection of cell lines.
SH   part
PR   CC   Part of
XP   /cell-line/comment-list/comment[@category="Part of"]
//
TG   population
DE   Ethnic group, nationality of the individual from which the cell line was sampled.
SH   pop
PR   CC   Population
XP   /cell-line/comment-list/comment[@category="Population"]
//
TG   problematic
DE   Known problem(s) related to the cell line: contaminated, misidentified, misclassified cell line or appearing in a retracted paper.
SH   prob
PR   CC   Problematic cell line
XP   /cell-line/comment-list/comment[@category="Problematic cell line"]
//
TG   resistance
DE   Selected to be resistant to some chemical compound (like a drug used in chemotherapy) or toxin. with a cross-reference to either ChEBI,
DE   DrugBank, NCIt or UniProtKB.
SH   res
PR   CC   Selected for resistance to
XP   /cell-line/resistance-list/resistance
//
TG   senescence
DE   When a finite cell line will senesce.
SH   sen
PR   CC   Senescence
XP   /cell-line/comment-list/comment[@category="Senescence"]
//
TG   integrated
DE   Genetic element(s) integrated in the cell line: gene name and identifier in CGNC, FlyBase, FPbase, HGNC, MGI, RGD, UniProtKB, and VGNC.
SH   int
PR   CC   Genetic integration
XP   /cell-line/genetic-integration-list/genetic-integration
//
TG   transformant
DE   What caused the cell line to be transformed: generally a virus (with a cross-reference to NCBI taxon identifier), a chemical compound
DE   (with a cross-reference to ChEBI) or a form of irradiation (with a cross-reference to NCIt).
SH   tfor
PR   CC   Transformant
XP   /cell-line/transformant-list/transformant
//
TG   virology
DE   Susceptibility of the cell line to viral infection, presence of integrated viruses or any other virology-related information.
SH   vir
PR   CC   Virology
XP   /cell-line/comment-list/comment[@category="Virology"]
//
TG   cc
DE   Comment(s). Any content described in fields 
DE   genome-ancestry, hla, registration, sequence-variation, anecdotal, biotechnology, breed, caution, characteristics, 
DE   discontinued, donor-info, doubling-time, from, group, karyotype, knockout, miscellaneous, 
DE   misspelling, mab-isotype, mab-target, msi, omics, population, problematic, resistance, senescence, transfected, transformant, virology.
PR   CC
XP   /cell-line/comment-list/comment
//
TG   str
DE   Short tandem repeat profile.
PR   ST
XP   /cell-line/str-list
CC   Pam: for solr index we miss the marker id attribute value
CC   For both the API and the full text search: no need to go deep in the structure
CC   of the STR profile: CLASTR is used for search in STR profiles and if one really wants
CC   to get cell lines with a specific STR value for a marker lets do that in SPARQL
//
TG   di
DE   Disease(s) suffered by the individual from which the cell line originated with its NCI Thesaurus or ORDO identifier.
PR   DI
XP   /cell-line/disease-list
//
TG   din
DE   Disease(s) suffered by the individual from which the cell line originated, restricted to diseases having a NCI Thesaurus identifier.
PR   DI   NCIt
XP   /cell-line/disease-list/xref[@database="NCIt"]
//
TG   dio
DE   Disease(s) suffered by the individual from which the cell line originated, restricted to diseases having an ORDO identifier.
PR   DI   ORDO
XP   /cell-line/disease-list/xref[@database="ORDO"]
//
TG   ox
DE   Species of the individual from which the cell line originates with its NCBI taxon identifier.
PR   OX
XP   /cell-line/species-list
CC   Pam: we miss the attribute values in solr indexes
//
TG   sx
DE   Sex of the individual from which the cell line originates.
PR   SX
XP   /cell-line/attribute::sex
//
TG   ag
DE   Age at sampling time of the individual from which the cell line was established.
PR   AG
XP   /cell-line/attribute::age
CC   Will stop being an attribute and become an XML element
CC   when links to developmental stage ontology are added
//
TG   oi
DE   Cell line(s) originating from same individual (sister cell lines).
PR   OI
XP   /cell-line/same-origin-as
//
TG   hi
DE   Parent cell line from which the cell line originates.
PR   HI
XP   /cell-line/derived-from
//
TG   ch
DE   Cell line(s) originated from the cell line (child cell lines).
PR   CH
XP   /cell-line/child-list/child
CC   Maybe create a new XML element <children-list>
CC   The only virtual field
CC   Pam: I chose <child-list> to be more consstent with other <...-list> elements
//
TG   ca
DE   Category to which a cell line belongs, one of 14 defined terms. Example: cancer cell line, hybridoma, transformed cell line.
PR   CA
XP   /cell-line/attribute::category
//
TG   dt
DE   Creation date, last modification date and version number of the cell line Cellosaurus entry.
PR   DT
XP   /cell-line/attribute::created
XP   /cell-line/attribute::last-updated
XP   /cell-line/attribute::entry-version
//
TG   dtc
DE   Creation date of the cell line Cellosaurus entry.
PR   DT
XP   /cell-line/attribute::created
//
TG   dtu
DE   Last modification date of the cell line Cellosaurus entry.
PR   DT
XP   /cell-line/attribute::last-updated
//
TG   dtv
DE   Version number of the cell line Cellosaurus entry.
PR   DT
XP   /cell-line/attribute::entry-version
//