Update GO Ontology Canis lupus familiaris

[Pauline P.]

Dear all,

Please excuse me if my question is silly - I'm a computer noob.

I'm trying to update the GO ontology for the species dog on ClueGO. Since I read it in multiple threats here, I have changed the links in the "properties" file:

##### General Settings #############################################################
organism.name = Canis Lupus Familiaris
organism.kegg.name = cfa
organism.taxid = 9615
organism.reactome.id = Canis familiaris
organism.wikipathway.id = Canis familiaris
####################################################################################

##### Settings for Gene2Accession update ###########################################
gene.info.url = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Canis_familiaris.gene_info.gz
gene2accession.url = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz
gene2ensembl.url = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz
organism.update.needs.special.treatment = false
####################################################################################

##### obo.ids should correspond to the obo.urls and to the association.urls !!! ####
##### For each obo.id you should have an obo.url and an association.url ############
obo.ids = GO
obo.urls = http://current.geneontology.org/ontology/go-basic.obo
association.urls = https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/4823216.C_lupus_familiaris_4.goa
#association.urls = https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Canis_lupus_familiaris/representative/GCF_011100685.1_UU_Cfam_GSD_1.0/GCF_011100685.1_UU_Cfam_GSD_1.0_gene_ontology.gaf.gz
####################################################################################

##### Select the Ontology roots to build/update your association files #############
ontology.roots = GO:0008150|BiologicalProcess;GO:0005575|CellularComponent;GO:0003674|MolecularFunction;GO:0002376|ImmuneSystemProcess
####################################################################################

##### Select the Ontology terms for CluePedia and the Cerebral Plugin to define ####
##### to define the cell layers and downstram genes ################################
##### The rules: ###################################################################
##### OntologyFileName(GO/KEGG/REACTOME)|[NumberOfLayer.]NameOfLayer;TermNames,[TermNames]#[[NumberOfLayer.]NameOfLayer;TermNames,[TermNames]]||[OntologyFileName(GO/KEGG/REACTOME)|[NumberOfLayer.]NameOfLayer;TermNames,[TermNames]#[[NumberOfLayer.]NameOfLayer;TermNames,[TermNames]]]
cerebral.localization.column = GO_CellularComponent_23.05.2012_16h07|1.Extracellular;GO:0031012,GO:0044420,GO:0044421,GO:0031012#2.Plasma Membrane;GO:0044425#3.Intra Cellular;GO:0044424#4.Nuclear Membrane;GO:0031965,GO:0044453#5.Nucleus;GO:0044428,GO:0005730,GO:0044452
cerebral.downstream.column = GO_CellularComponent_23.05.2012_16h07|Transcription Factor Complex;GO:0005667
####################################################################################

 The problem is, that it didn't update all of the GO categoriez, just one categorie called "ImmuneSystemProcess-Custom", that only contains one term.

I hope someone can help me :)

Thanks in advance,

Pauline

[Scooter Morris]

Hi Pauline,

I would reach out to the ClueGO authors directly.  They are usually very responsive.

-- scooter