python library for working with ontologies and ontology associations
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Add ns2:evidence-with property to models that have been converted to 'has_input' edges. #566
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sierra-moxon closed 3 years ago
From David H. (also happening in the ZFIN import)
When an annotation is made in the conventional way to a protein binding term, the binding partner is put in the 'inferred from/with' field of the GPAD file. This is converted in an input of the binding in a GO-CAM model. We need to convert it back to the 'inferred from/with' field so the annotations match the old convention. See examples below: https://urldefense.com/v3/__http://noctua-dev.berkeleybop.org/editor/graph/gomodel:MGI_MGI_2441920__;!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPhyQBufko$
input GPAD2.0 MGI:MGI:2441920 RO:0002327 GO:0005515 MGI:MGI:5574544|PMID:24843136 ECO:0000353 PR:P70338|PR:O70237 2015-04-24 MGI creation-date=2015-04-24|modification-date=2015-04-24|contributor-id=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306__;!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPhxXs-hyO$
MGI:MGI:2441920 RO:0002327 GO:0019899 MGI:MGI:5574544|PMID:24843136 ECO:0000353 PR:Q6ZQ88 2015-04-24 MGI creation-date=2015-04-24|modification-date=2015-04-24|contributor-id=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306__;!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPhxXs-hyO$
Noctua output GPAD1.1 (Note that the pipe-delimited with field is also correctly split into two annotations) MGI MGI:2441920 enables GO:0005515 PMID:24843136|MGI:MGI:5574544 ECO:0000353 20150424 MGI has_input(PR:P70338) contributor=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306*7Cnoctua-model-id=gomodel:MGI_MGI_2441920*7Cmodel-state=development__;JSU!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPh_pixlUP$ MGI MGI:2441920 enables GO:0005515 MGI:MGI:5574544|PMID:24843136 ECO:0000353 20150424 MGI has_input(PR:O70237) contributor=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306*7Cnoctua-model-id=gomodel:MGI_MGI_2441920*7Cmodel-state=development__;JSU!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPh_pixlUP$ MGI MGI:2441920 enables GO:0019899 PMID:24843136|MGI:MGI:5574544 ECO:0000353 20150424 MGI has_input(PR:Q6ZQ88) contributor=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306*7Cnoctua-model-id=gomodel:MGI_MGI_2441920*7Cmodel-state=development__;JSU!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPh_pixlUP$
This output should be: MGI MGI:2441920 enables GO:0005515 PMID:24843136|MGI:MGI:5574544 ECO:0000353 PR:P70338 20150424 MGI contributor=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306*7Cnoctua-model-id=gomodel:MGI_MGI_2441920*7Cmodel-state=development__;JSU!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPh_pixlUP$ MGI MGI:2441920 enables GO:0005515 MGI:MGI:5574544|PMID:24843136 ECO:0000353 PR:O70237 20150424 MGI contributor=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306*7Cnoctua-model-id=gomodel:MGI_MGI_2441920*7Cmodel-state=development__;JSU!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPh_pixlUP$ MGI MGI:2441920 enables GO:0019899 PMID:24843136|MGI:MGI:5574544 ECO:0000353 PR:Q6ZQ88 20150424 MGI contributor=https://urldefense.com/v3/__http://orcid.org/0000-0001-7476-6306*7Cnoctua-model-id=gomodel:MGI_MGI_2441920*7Cmodel-state=development__;JSU!!C5qS4YX3!XPuTk7YPGZkjcq1wIlpH4MMAk2qLoihBBlXCSs9ilwJyh2JrKdPq33UPh_pixlUP$