7 Jan 2020 PAINT Conference Call: Difference between revisions
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* Pascale: The dataset yaml files describe all sources that provide their own namespaces: https://github.com/geneontology/go-site/tree/master/metadata/datasets | * Pascale: The dataset yaml files describe all sources that provide their own namespaces: https://github.com/geneontology/go-site/tree/master/metadata/datasets | ||
* We noted that in the two links above, the species is different: Aspergillus fumigatus Af293 (Taxid:330879) for IBA annotations and Aspergillus fumigatus (Taxid:746128) | * We noted that in the two links above, the species is different: Aspergillus fumigatus Af293 (Taxid:330879) for IBA annotations and Aspergillus fumigatus (Taxid:746128) | ||
* | * From the RefProt README file that we use to map 5-letter code to taxon ID ASPFU->330879: | ||
[UP000002530 330879 ASPFU 9647 0 9652 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (Aspergillus fumigatus)] | |||
3. Taxon constraints in PAINT | 3. Taxon constraints in PAINT | ||
Revision as of 13:27, 7 January 2020
Present
Pascale, Huaiyu, Dustin, Anushya
Discussion points
1. I think Dustin has some data/forward tracking issues he’d like to discuss: Dustin, would you please list those or send links to tickets ?
2. I would like to discuss the ID space that we use - for example for AspGD we are using UniProt, so Aspergillus has some annotations as ASPDG IDs, and IBAs as UniProt. We should be using a single ID space for each species.
See for example:
- http://amigo.geneontology.org/amigo/gene_product/AspGD:ASPL0000109327
- http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E9R876
Discussion:
- Huaiyu: Consortium needs to provide guidelines for name spaces for each species.
- Pascale: The dataset yaml files describe all sources that provide their own namespaces: https://github.com/geneontology/go-site/tree/master/metadata/datasets
- We noted that in the two links above, the species is different: Aspergillus fumigatus Af293 (Taxid:330879) for IBA annotations and Aspergillus fumigatus (Taxid:746128)
- From the RefProt README file that we use to map 5-letter code to taxon ID ASPFU->330879:
[UP000002530 330879 ASPFU 9647 0 9652 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (Aspergillus fumigatus)]
3. Taxon constraints in PAINT