kltm
It would be nice to look at the current AmiGO load "http://skyhook.berkeleybop.org/master/ontology/extensions/go-gaf.owl", "http://skyhook.berkeleybop.org/master/ontology/extensions/gorel.owl", "http://skyhook.berkeleybop.org/master/ontology/extensions/go-modules-annotations.owl", "http://skyhook.berkeleybop.org/master/ontology/extensions/go-taxon-subsets.owl", "http://purl.obolibrary.org/obo/eco/eco-basic.owl", "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl", "http://purl.obolibrary.org/obo/cl/cl-basic.owl", "http://purl.obolibrary.org/obo/pato.owl", "http://purl.obolibrary.org/obo/po.owl", "http://purl.obolibrary.org/obo/chebi.owl", "http://purl.obolibrary.org/obo/uberon/basic.owl", "http://purl.obolibrary.org/obo/wbbt.owl" It would be good to do for...
Given that there are many URLs in the wild like http://www.obofoundry.org/cgi-bin/detail.cgi?id=brenda , it would be best to configure the GitHub Pages 404s to either contain a search, an explanation and...
The case we ran into here was parsing the goa_uniprot_all.gaf.gz file for the GO. Specifically: ```bash ontobio-parse-assocs.py -f /opt/go-site/annotations/goa_uniprot_all.gaf -F gaf -o /opt/go-site/annotations_new/goa_uniprot_all.gaf -I /opt/go-site/gaferencer-products/all.gaferences.json --report-md /tmp/report.md --report-json /tmp/report.json convert...
_From @murphyte on July 6, 2018 20:23_ Hi GO -- Some data files have recently shown a change where column 13 has the string "NCBITaxon:" with no value for some...
As it stands now, there is no way of knowing what calls are coming from biolink/ontobio except by knowing IP addresses. It should be standard to have all HTTP calls...
OWLTools testing cleaning and updates around ECO, with the context of work on geneontology/pipeline#251.
Loading GAF 2.2-centric files into owltools, then looking at the produced index, for annotation, the only qualifiers listed were: ``` (38043) | contributes_to (11469) | not (11363) | colocalizes_with ```...
Correct label and biological process issues for model annotation loader, possible other improvements
Looking at the output of a loader run: http://tomodachi.berkeleybop.org/amigo/search/model_annotation The values in the return documents that drive this interface are like: ```json { "document_category":"model_annotation", "id":"gomodel:581e072c00000062|http://model.geneontology.org/581e072c00000062/581e072c00000098|FB:FBgn0005672|GO:0048019|", "annotation_unit":"gomodel:581e072c00000062|http://model.geneontology.org/581e072c00000062/581e072c00000098|FB:FBgn0005672|GO:0048019|", "annotation_unit_label":"gomodel:581e072c00000062 spi Dmel GO:0048019",...
I believe that currently owltools would not support the upcoming GAF 2.2 spec particularly well. While the only material difference for the new spec is that many more qualifiers are...
We'd like to decommission the machines currently supporting code.berkeleybop.org. As an approach, we'd like to do this using GitHub to support the Maven repo. See: https://stackoverflow.com/questions/14013644/hosting-a-maven-repository-on-github Note a previous WIP...