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/similarity/frequency returns nothing at least for some phenotypes for the genes corpus #192

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hlapp opened this issue Feb 17, 2020 · 1 comment · Fixed by #206
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/similarity/frequency returns nothing at least for some phenotypes for the genes corpus #192

hlapp opened this issue Feb 17, 2020 · 1 comment · Fixed by #206
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hlapp commented Feb 17, 2020 •
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For example, the following yields a row for the taxa corpus:

curl -X GET "https://kb.phenoscape.org/api/similarity/frequency?terms=%5B%22http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000051%253E%2Bsome%2B%250A%2B%2B%2B%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPATO_0001955%253E%250A%2B%2B%2B%2B%2Band%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000052%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_2002077%253E%2529%2529%22%5D&corpus_graph=http%3A%2F%2Fkb.phenoscape.org%2Fsim%2Ftaxa" -H "accept: text/csv"

However, when switching to the genes corpus, it yields zero bytes:

curl -X GET "https://kb.phenoscape.org/api/similarity/frequency?terms=%5B%22http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000051%253E%2Bsome%2B%250A%2B%2B%2B%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPATO_0001955%253E%250A%2B%2B%2B%2B%2Band%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000052%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_2002077%253E%2529%2529%22%5D&corpus_graph=http%3A%2F%2Fkb.phenoscape.org%2Fsim%2Fgenes" -H "accept: text/csv"

Even a phenotype associated with a gene (http://zfin.org/ZDB-GENE-040426-731, brpf1) yields nothing:

as.phenotype("http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051%3E+some+%0A++++%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001483%3E%0A+++++and+%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000052%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FZFA_0000316%3E%29%29")$label
[1] "basihyal bone aplastic"
curl -X GET "https://kb.phenoscape.org/api/similarity/frequency?terms=%5B%22http%3A%2F%2Fpurl.org%2Fphenoscape%2Fexpression%3Fvalue%3D%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000051%253E%2Bsome%2B%250A%2B%2B%2B%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPATO_0001483%253E%250A%2B%2B%2B%2B%2Band%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000052%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FZFA_0000316%253E%2529%2529%22%5D&corpus_graph=http%3A%2F%2Fkb.phenoscape.org%2Fsim%2Fgenes" -H "accept: text/csv"

Is the endpoint broken for the genes corpus, or does it expect a different kind of input term?
hlapp added a commit to phenoscape/rphenoscape that referenced this issue Feb 18, 2020
@hlapp
Adds ability to obtain or calculate term frequencies
330fc7d 
Note that not all corpora are supported in the KB API yet. Specifically,
support for the "gene_annotations" corpus is pending in the API
(see phenoscape/phenoscape-kb-services#146 and phenoscape/phenoscape-kb-services#189),
and at least presently there are some issues in the KB API for the "genes"
corpus (see phenoscape/phenoscape-kb-services#191 and
phenoscape/phenoscape-kb-services#192).
This was referenced Feb 18, 2020
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hlapp commented Feb 18, 2020

Show this issue's status in phenoscape/rphenoscape#139.

@Shalsh23 Shalsh23 mentioned this issue Mar 13, 2020
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Add implementation for similarity/frequency for genes corpus phenoscape/phenoscape-kb-services
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