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curie_map.yaml
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curie_map.yaml
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# NO EMPTY
? ''
: file:///ERROR/EMPTY/PREFIX/BANNED/
# rdf and friends
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#
owl: http://www.w3.org/2002/07/owl#
skos: http://www.w3.org/2004/02/skos/core#
foaf: http://xmlns.com/foaf/0.1/
prov: http://www.w3.org/ns/prov#
doap: http://usefulinc.com/ns/doap#
dc: http://purl.org/dc/elements/1.1/
dcterms: http://purl.org/dc/terms/
dctypes: http://purl.org/dc/dcmitype/ # FIXME there is no agreement on qnames
# base
NIFSTD: http://uri.neuinfo.org/nif/nifstd/
# NIFSTD namespaces
BIRNLEX: http://uri.neuinfo.org/nif/nifstd/birnlex_
NIFEXT: http://uri.neuinfo.org/nif/nifstd/nifext_
NIFRID: http://uri.neuinfo.org/nif/nifstd/readable/
NLX: http://uri.neuinfo.org/nif/nifstd/nlx_
NLXANAT: http://uri.neuinfo.org/nif/nifstd/nlx_anat_
NLXBR: http://uri.neuinfo.org/nif/nifstd/nlx_br_
NLXCELL: http://uri.neuinfo.org/nif/nifstd/nlx_cell_
NLXCHEM: http://uri.neuinfo.org/nif/nifstd/nlx_chem_
NLXDYS: http://uri.neuinfo.org/nif/nifstd/nlx_dys_
NLXFUNC: http://uri.neuinfo.org/nif/nifstd/nlx_func_
NLXINV: http://uri.neuinfo.org/nif/nifstd/nlx_inv_
NLXMOL: http://uri.neuinfo.org/nif/nifstd/nlx_mol_
NLXNEURNT: http://uri.neuinfo.org/nif/nifstd/nlx_neuron_nt_
NLXOEN: http://uri.neuinfo.org/nif/nifstd/oen_
NLXORG: http://uri.neuinfo.org/nif/nifstd/nlx_organ_
NLXQUAL: http://uri.neuinfo.org/nif/nifstd/nlx_qual_
NLXRES: http://uri.neuinfo.org/nif/nifstd/nlx_res_
NLXSUB: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_
NLXUBO: http://uri.neuinfo.org/nif/nifstd/nlx_ubo_
NLXUNCL: http://uri.neuinfo.org/nif/nifstd/nlx_uncl_
SAO: http://uri.neuinfo.org/nif/nifstd/sao
# interlex
ILX: http://uri.interlex.org/base/ilx_
#CDE: http://uri.interlex.org/base/cde_ # needs to be updated to ILX.CDE
ILX.CDE: http://uri.interlex.org/base/cde_
ilx: http://uri.interlex.org/ # NOTE no /base/
ilxr: http://uri.interlex.org/base/readable/
TEMP: http://uri.interlex.org/temp/uris/
ILXREPLACE: http://ILXREPLACE.org/
# interlex user/org namespaces
MIRO: http://uri.interlex.org/MIRO/uris/readable/
DICOM: http://uri.interlex.org/dicom/uris/terms/
PAR: http://uri.interlex.org/fakeobo/uris/obo/PAR_
PAXRAT: http://uri.interlex.org/paxinos/uris/rat/labels/
PAXMUS: http://uri.interlex.org/paxinos/uris/mouse/labels/
PAXSPN: http://uri.interlex.org/paxinos/uris/spine/labels/
pax: http://uri.interlex.org/paxinos/uris/
pax.mus: http://uri.interlex.org/paxinos/uris/mouse/
pax.mus.ver: http://uri.interlex.org/paxinos/uris/mouse/versions/
pax.rat: http://uri.interlex.org/paxinos/uris/rat/
pax.rat.ver: http://uri.interlex.org/paxinos/uris/rat/versions/
aibs.hum.ver: http://uri.interlex.org/aibs/uris/human/versions/
aibs.mus.lab: http://uri.interlex.org/aibs/uris/mouse/labels/
aibs.mus.ver: http://uri.interlex.org/aibs/uris/mouse/versions/
fsl.ats: http://uri.interlex.org/fsl/uris/atlases/
hcp.mmp.ver: http://uri.interlex.org/hcp/uris/mmp/versions/
wax.sd.ver: http://uri.interlex.org/waxholm/uris/sd/versions/
NDA.CDE: http://uri.interlex.org/NDA/uris/datadictionary/elements/
ilxtr: http://uri.interlex.org/tgbugs/uris/readable/
ilxti: http://uri.interlex.org/tgbugs/uris/indexes/
ilxtib: http://uri.interlex.org/tgbugs/uris/indexes/blank/
ilxtio: http://uri.interlex.org/tgbugs/uris/indexes/ontologies/
build: http://uri.interlex.org/tgbugs/uris/readable/build/
buildid: http://uri.interlex.org/tgbugs/uris/readable/build/id/
npokb: http://uri.interlex.org/npo/uris/neurons/
mmset1: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/mmset1/
mmset2cn: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/mmset2cn/
mmset3: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/mmset3/
mmset4: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/mmset4/
semves: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/semves/
prostate: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/prostate/
femrep: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/femrep/
senmot: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/senmot/
swglnd: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/swglnd/
liver: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/liver/
kidney: http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/kidney/
atom: http://uri.interlex.org/tgbugs/uris/readable/atlas/
PRECISETBI.CDE: http://uri.interlex.org/precise-tbi/uris/cde/
# alternate ids
GBIF: http://www.gbif.org/species/
ITISTSN: http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=
MESH: https://meshb.nlm.nih.gov/record/ui?ui=
RadLex: http://www.radlex.org/RID/ # matches uberon
SBO: 'http://www.ebi.ac.uk/sbo/main/SBO:' # SBO is a fakeobo
# scicrunch registry
SCR: http://scicrunch.org/resolver/SCR_
# scicrunch rrid resolver
RRID: 'https://scicrunch.org/resolver/RRID:'
# ontologies
obo: http://purl.obolibrary.org/obo/
HP: http://purl.obolibrary.org/obo/HP_
RO: http://purl.obolibrary.org/obo/RO_
OBI: http://purl.obolibrary.org/obo/OBI_
oboInOwl: http://www.geneontology.org/formats/oboInOwl#
IAO: http://purl.obolibrary.org/obo/IAO_
SO: http://purl.obolibrary.org/obo/SO_
BFO: http://purl.obolibrary.org/obo/BFO_
DOID: http://purl.obolibrary.org/obo/DOID_
MONDO: http://purl.obolibrary.org/obo/MONDO_
PATO: http://purl.obolibrary.org/obo/PATO_
EMAPA: http://purl.obolibrary.org/obo/EMAPA_
PR: http://purl.obolibrary.org/obo/PR_
PW: http://purl.obolibrary.org/obo/PW_
CL: http://purl.obolibrary.org/obo/CL_
MA: http://purl.obolibrary.org/obo/MA_
MP: http://purl.obolibrary.org/obo/MP_
CLO: http://purl.obolibrary.org/obo/CLO_
GO: http://purl.obolibrary.org/obo/GO_
SIO: http://semanticscience.org/resource/SIO_
EFO: http://www.ebi.ac.uk/efo/EFO_
SWO: http://www.ebi.ac.uk/efo/swo/SWO_
SWOL: http://www.ebi.ac.uk/swo/license/SWO_
UBERON: http://purl.obolibrary.org/obo/UBERON_
ERO: http://purl.obolibrary.org/obo/ERO_
NCBIGene: http://www.ncbi.nlm.nih.gov/gene/
NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
UO: http://purl.obolibrary.org/obo/UO_
CHEBI: http://purl.obolibrary.org/obo/CHEBI_
chebi: http://purl.obolibrary.org/obo/chebi/
FMA: http://purl.org/sig/ont/fma/fma
fma: http://purl.org/sig/ont/fma/
# AIBS api endpoints
HBA: 'http://api.brain-map.org:80/api/v2/data/Structure/' # FIXME hack :/
MBA: http://api.brain-map.org/api/v2/data/Structure/
AIBSTL: http://api.brain-map.org/api/v2/data/TransgenicLine/ # FIXME see what we did locally
AIBSSPEC: http://api.brain-map.org/api/v2/data/Specimen/
#NEMOANN: http://purl.bioontology.org/NEMO/ontology/NEMO_annotation_properties.owl
#NEMO: http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_
BFO1: http://www.ifomis.org/bfo/1.1#
BFO1SNAP: http://www.ifomis.org/bfo/1.1/snap#
BFO1SPAN: http://www.ifomis.org/bfo/1.1/span#
CAO: http://www.cognitiveatlas.org/ontology/cogat.owl#CAO_
COGAT: http://www.cognitiveatlas.org/ontology/cogat.owl#
COGPO: http://www.cogpo.org/ontologies/COGPO_ # doesn't resolve
COGPO1: http://www.cogpo.org/ontologies/CogPOver1.owl#COGPO_
COGPO10: http://www.cogpo.org/ontologies/CogPOver2010.owl#COGPO_
TRANS: http://purl.obolibrary.org/obo/TRANS_
SYMP: http://purl.obolibrary.org/obo/SYMP_
# NIF Import closure
BIRNANN: http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#
BIRNOBI: http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#
BIRNOBO: http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#
#NIFBE: http://ontology.neuinfo.org/NIF/Backend/nif_backend.owl#
NIFQUAL: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Quality.owl#
OBOANN: http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#
NIFANN: http://ontology.neuinfo.org/NIF/NIF-Annotation-Standard.owl#
NIFCELL: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl#
NIFCHEM: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Chemical.owl#
NIFGA: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#
NIFMOL: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#
NIFORG: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl#
NIFSUB: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#
NIFUNCL: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Unclassified.owl#
SAOCORE: http://ontology.neuinfo.org/NIF/BiomaterialEntities/SAO-CORE_properties.owl#
NIFGG: http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Government-Granting-Agency.owl#
NIFINV: http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#
NIFRES: http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Resource.owl#
NIFSCID: http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#
NIFDYS: http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#
NIFFUN: http://ontology.neuinfo.org/NIF/Function/NIF-Function.owl#
# Inferred or Slim
NIFMOLINF: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule-Role-Inferred.owl#
NIFNCBISLIM: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-NCBITaxonomy-Slim.owl#
# Bridge
#QUALBB: http://ontology.neuinfo.org/NIF/Backend/quality_bfo_bridge.owl#
#NIFERO: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Eagle-I-Bridge.owl#
#NIFGOCC: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GO-CC-Bridge.owl#
NIFMOLROLE: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule-Role-Bridge# #AAAAAAA
NIFNCBI: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-NCBITax-Bridge.owl#
NIFNEURMC: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF_Neuron_MolecularConstituent_Bridge.owl#
NIFNEURBR: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-BrainRegion-Bridge.owl#
NIFNEURBR2: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Brain-Bridge.owl# #AAAAAAAA
NIFNEURCIR: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Circuit-Role-Bridge.owl#
NIFNEURMOR: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Morphology-Bridge.owl#
NIFNEURNT: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-NT-Bridge.owl#
# ApiNATOMY
apinatomy: https://apinatomy.org/uris/readable/
elements: https://apinatomy.org/uris/elements/
aacar: https://apinatomy.org/uris/models/ard-arm-cardiac/ids/
bolew: https://apinatomy.org/uris/models/bolser-lewis/ids/
kblad: https://apinatomy.org/uris/models/keast-bladder/ids/
bromo: https://apinatomy.org/uris/models/bronchomotor/ids/
scaft: https://apinatomy.org/uris/models/scaffold-test/ids/
vagnr: https://apinatomy.org/uris/models/vagus-nerve/ids/
sdcol: https://apinatomy.org/uris/models/sawg-distal-colon/ids/
sstom: https://apinatomy.org/uris/models/sawg-stomach/ids/
dlcon: https://apinatomy.org/uris/models/dev-layout-conn/ids/
splen: https://apinatomy.org/uris/models/spleen/ids/
pancr: https://apinatomy.org/uris/models/pancreas/ids/
smint: https://apinatomy.org/uris/models/small-intestine/ids/
# identifiers
PMID: http://www.ncbi.nlm.nih.gov/pubmed/
doi: https://doi.org/
# resource prefixes
JAX: http://jaxmice.jax.org/strain/ # FIXME redirects to http://www.jax.org/strain/ ... but that seems to be the preferred id ?
#JAXw: http://www.jax.org/strain/ # copy paste issue we should not have this as a compact form unless we do a full switchover
MMRRC: http://www.mmrrc.org/catalog/getSDS.jsp?mmrrc_id=