---------------------------------------------------------------------------- Pentacon NSAID Project Curation Princeton University, NJ, USA University of Pennsylvania, PA, USA ---------------------------------------------------------------------------- Readme file name: Curation_AAP_Mus-musculus_Readme_20140421_production.txt Readme for the following files: Curation_AAP_Mus-musculus_All_Topics_20140421_production.txt Total Number of Genes: 12 Corresponding gene file: Orthologs_and_Analogs _20140421_production.txt Version: production Date: 4/21/14 Curation Overview ----------------- Curation was performed by Pentacon curators based on information available in the published literature. The curation process involved selecting Arachidonic Acid Pathway genes of interest from reviews and curating tissue, cell line/type, disease, and GO molecular function data from the reviews and the supporting primary experimental evidence. Curators converted information found in the literature into standardized ontology terms and corresponding IDs that could be used in a computational analysis. This was done in a Google spreadsheet using OntoMaton. Information concerning OntaMaton is available here: http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/ Gene Lists: ----------- The curation in this file has been carried out for selected genes listed in the associated Orthologs_and_Analogs _20140421_production.txt. for the organism Mus musculus Curation Topics and Ontologies: ------------------------------- Curation Topic: Any conditional (drug) Conversion to Ontology: ChEBI Ontology: http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi Curation Topic: Any conditional (environmental) Conversion to Ontology: PATO Ontology: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PATO Curation Topic: Cell-type specificity/dependency Ontology: Cell Ontology Ontology URL: http://purl.obolibrary.org/obo/cl.owl Curation Topic: Cell line Conversion to Ontology: Cell Line Ontology/BRENDA Tissue Ontology Ontology: Cell Line Ontology Ontology URL: http://purl.obolibrary.org/obo/cl.owl Ontology: BRENDA Tissue Ontology Ontology URL: http://purl.bioontology.org/ontology/BTO Curation Topic: Cellular location Conversion to Ontology: GO Cellular Component Ontology: http://www.obofoundry.org/cgi-bin/detail.cgi?id=cellular_component Curation Topic: Pathway Conversion to Ontology: GO Biological Process Ontology: http://www.obofoundry.org/cgi-bin/detail.cgi?id=biological_process Curation Topic: Human Disease Conversion to Ontology: Human Disease Ontology Ontology URL: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DOID Other Ontology: SNOMED Other Ontology URL: http://purl.bioontology.org/ontology/SNOMEDCT Curation Topic: Tissue specificity/dependency Conversion to Ontology: Brenda Tissue Ontology Ontology URL: http://purl.bioontology.org/ontology/BTO Other Ontology: Uberon Other Ontology URL: http://purl.bioontology.org/ontology/UBERON Curation Topic: Developmental stage Conversion to Ontology: Brenda Tissue Ontology Ontology URL: http://purl.bioontology.org/ontology/BTO Other Ontology: Human Developmental Anatomy Ontology Other Ontology URL: not used Curation Topic: Phenotypes Conversion to Ontology: Human Phenotype Ontology Ontology URL: Not used for human disease phenotypes Curation Topic: Isoforms Conversion to Ontology: None Ontology URL: None Secondary IDs: UniProt VSP_ IDs Curation Topic: Variants/Genetic Background Conversion to Ontology: None Ontology URL: None Secondary IDs: UniProt VAR_ IDs and dbSNP rs IDs Curation Topic: Kinetics Conversion to Ontology: None Ontology URL: None Curation files: ---------------------- Curation_AAP_Mus-musculus_All_Topics_20140421_production.txt All curation topics above except for isoforms, variants and kinetics ---------------------------------------------------------------------------- (---Notes provided for specific columns where applicable.) Curator Name UniProt ID NCBI Gene ID Gene Name Species Name Taxonomy ID Data Type ---See curation topics above Data Value ---Text summarized or quoted from the literature added by a PENTACON curator. GO Term --- GO MF terms (possibly some GO CC or BP terms). GO ID Uberon Term Uberon ID BRENDA Tissue Ontology Term BRENDA Tissue Ontology ID Anatomy Ontology Term Anatomy Ontology ID Phenotype Ontology Term Phenotype Ontology ID Developmental Stage Term (BRENDA) Developmental Stage ID (BRENDA) Cell Type Ontology Term (CTO or CL) Cell Type Ontology ID (CTO or CL) Cell Line Ontology Term (CLO) Cell Line Ontology ID (CLO) PATO Qualifier PATO ID OMIM ID Human Disease Ontology Term Human Disease Ontology ID SNOMED Term ---Added if no applicable Human Disease Ontology term found SNOMED ID ChEBI Chemical Term ChEBI Chemical ID Secondary Source IDs --- Not used in this curation Secondary Source Notes --- Not used in this curation Reviewed (Y/N) --- Reviewed by a Pentacon curator (Y=yes, N=no) Use (Y/N) ---Curation for that row is valid and can be used (Y=yes, N=no) Evidence Code ---Evidence Code Ontology ID (ECO:0000311 = Imported Information, ECO:0000006 = Experimental, ECO:0000033 = traceable author statement, ECO:0000035 = no biological data found) Primary Source ---Typically the PubMed ID Secondary Source ---Secondary Source = Pentacon, the curated information and ontology terms were added by Pentacon curators and associated with relevant PubMed IDs. PENTACON Notes --- Pentacon curator notes; may contain relevant citation information for the associated papers. If the primary paper was traced from a review of interest the review will be cited in this column. May contain additional notes Gene Set ---Abbreviation used to indicate the corresponding gene collection relevant to a certain biological pathway or network, e.g. AAP is used for genes directly involved in the 'arachidonic acid pathway', AAE is used for genes related to the arachidonic acid pathway, and BP refers to genes related to the phenotype of blood pressure. Secondary Source Version Date ---Date originally released by PENTACON Secondary Source Version ---Version number of original release by PENTACON PENTACON Annotation No ---Unique annotation ID assigned by Pentacon. ---------------------------------------------------------------------------- For questions please contact Rose Oughtred (rose at genomics.princeton.edu). ----------------------------------------------------------------------------