save afp_species list in pap_species

WormBase / ACKnowledge

Author Curation to Knowledgebases

MIT License

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save afp_species list in pap_species #38

Closed valearna closed 5 years ago

valearna commented 5 years ago

merge existing data with new one - keep existing data and do not replicate rows with afp data. Add afp data if not already present
no evidence
use taxon id and put order at the end
do we need to create a person id for afp? - we need to change the pipeline and process only papers that have an email address linked to a person ID. We can test all addresses in the paper and if none is linked to a person ID we skip the paper
save information to h_pap_species as well - when deleting data we have to add new records with blank lines (pap_gene column set to null)

valearna commented 5 years ago

@vanaukenk I can't find the person ID for afp. If I'm not wrong we verified that it was already there in the system during the last meeting

vanaukenk commented 5 years ago

@valearna There isn't already a person ID for afp. Let's chat with @azurebrd about this, as he had some suggestions for what we could do.

valearna commented 5 years ago

http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/phenotype.cgi?action=autocompleteXHR&field=person&query=bob

http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/phenotype.cgi?action=asyncTermInfo&field=person&termid=WBPerson3528

Combine these API calls in a new component to select the person ID with which results will be saved

valearna commented 5 years ago

save pap_curator in the form 'two\<PersonID>' instead of 'WBPerson\<PersonID>'

valearna commented 5 years ago

The table pap_species doesn't have a field for evidence codes. Keeping track of the species when authors save the AFP form multiple times after removing previously selected species is quite complicated. Can we add a pap_evidence field as in the pap_gene table @azurebrd ?

azurebrd commented 5 years ago

Resolved in emails. The ?Paper -> ?Gene connection in the acedb model has an #Evidence while ?Paper -> ?Species doesn't, so we'll do updates based on paper-curator-data

vanaukenk commented 5 years ago

There is #Evidence for the ?Species tag in the ACeDB ?Paper model, so perhaps the best thing to do would be to add a pap_evidence column to the pap_species table in postgres and, going forward, populate that similarly to how we populate pap_evidence for pap_gene.

https://wormbase.org/tools/tree/run?name=%3FPaper;class=Model;expand=Refers_to#Refers_to