pgaudet

Fix eco-usage-constraint file to support GOEx pipeline

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For the GOEx pipeline we are missing a standard way in which the allowed GO_REFs for each ECO code is described. @alexsign and I will add this information to :...

New GOA pipeline report: strip redundant Noctua annotations when loading in GOA

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If there already is the same annotation in GOA, then the Noctua GPAD line is not loaded. Data taken into account: **- Two annotations are considered redundant if:** - Same...

Currently, With/From: IC annotations require a With/From GO ID is a 'report', not a hard filter. https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000016.md @hattrill proposes to make it a hard filter

https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000059.md is a duplicate of https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000061.md GORULE:0000059 is more complete.

See https://github.com/geneontology/go-site/blob/master/metadata/biological_entity_mapping.yaml

Fix TAIR cross references

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Hi @kltm Our links to TAIR internal references are not correct, see examples in this page: https://amigo.geneontology.org/amigo/gene_product/AGI_LocusCode:AT1G77890 From @tberardini Communication: http://arabidopsis.org/servlets/TairObject?accession=Communication:1345790 should be https://www.arabidopsis.org/communication?key=1345790 Analysis Reference: http://arabidopsis.org/servlets/TairObject?accession=AnalysisReference:501780126 should be https://www.arabidopsis.org/analysisreference?key=501780126

For the GOEx pipeline, we need all references mapped to an object known to the pipeline, so we need to create a GOREF for [TAIR:AnalysisReference:501780126](https://www.arabidopsis.org/analysisreference?key=501780126) @alexsign - id: GO_REF:0000122 title:...

Hi, The ZFIN syntax check by GOA is identifying entities that are not in the ZFIN dbxref list: |CRISPR|FISH|TALEN For example: > ZFIN ZDB-GENE-041111-255 acts_upstream_of_or_within GO:0010481 PMID:28199303 ECO:0000315 ZFIN:ZDB-CRISPR-170908-2 20180117...

For example case should be fixed: - FLYBASE should be repaired to FlyBase - UniProtKB should not be allowed - it's UniProt) (these are coming from EcoCyc GAF. Note there...