From 8d5952632c025b12f90f9ce6bfdb22b7e6dad046 Mon Sep 17 00:00:00 2001 From: Nils Hoffmann <3309580+nilshoffmann@users.noreply.github.com> Date: Wed, 4 May 2022 08:26:07 +0200 Subject: [PATCH] Updated ontology URLs to obofoundry links Addressing issue #205 to provide stable URL for recommended ontologies. --- ...ab_format_specification_2_0-M_release.adoc | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc b/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc index 02ccb3e4..e074115c 100644 --- a/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc +++ b/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc @@ -147,16 +147,19 @@ As recommended by the PSI CV guidelines, psi-ms.obo should be dynamically mainta The following ontologies or controlled vocabularies specified below may also be recommended or required in certain instances, as specified within the https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-developments/2_0-Metabolomics-Draft/mzTab_2_0-M_mapping.xml[CV mapping file]: -* Unit Ontology (http://www.obofoundry.org/ontology/uo.html) -* ChEBI (ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo) -* OBI Ontology of Biological Investigations (http://obi-ontology.org/) -* NCBITaxon UniProt Taxonomy Database (https://www.ebi.ac.uk/ols/ontologies/ncbitaxon) -* BRENDA tissue/ enzyme source (http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO). -* Cell Type ontology (https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-basic.obo). -* Human disease ontology (http://www.disease-ontology.org/). -* XLMOD ontology with chemical reagents used for cross-linking and derivatization (https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo). +* Unit Ontology (https://obofoundry.org/ontology/uo.html). +* ChEBI (https://obofoundry.org/ontology/chebi.html). +* OBI Ontology of Biological Investigations (https://obofoundry.org/ontology/obi.html). +* NCBITaxon UniProt Taxonomy Database (https://obofoundry.org/ontology/ncbitaxon.html). +* BRENDA tissue/ enzyme source (https://obofoundry.org/ontology/bto.html). +* Cell Type ontology (https://obofoundry.org/ontology/cl.html). +* Human disease ontology (https://obofoundry.org/ontology/doid.html). +* XLMOD ontology with chemical reagents used for cross-linking and derivatization (https://obofoundry.org/ontology/xlmod.html). * PRIDE (Proteomics Identifications) ontology (https://github.com/PRIDE-Utilities/pride-ontology). * MSIO (Metabolomics Standards Initiative) ontology (https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO) for metabolomics, including harvesting, material and sample processing. +* NCIT (NCI Thesaurus) (https://obofoundry.org/ontology/ncit.html) NCI Thesaurus (NCIt) is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. + +Most of these ontologies are also indexed and searchable at EBI's Ontology Lookup Service (OLS) at https://www.ebi.ac.uk/ols/index [[resolved-design-and-scope-issues]] == Resolved Design and scope issues