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Bug in /similarity/frequency? #191

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hlapp opened this issue Feb 15, 2020 · 3 comments
Closed

Bug in /similarity/frequency? #191

hlapp opened this issue Feb 15, 2020 · 3 comments
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@hlapp
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hlapp commented Feb 15, 2020

The following phenotype is linked to 4 taxa:

Phenotype 'basibranchial 2 bone interlocked with basihyal bone'
Linked to states:
                                                                                                                label
1 second basibranchial  present but reduced, posteriorly acuminate, and interlocked with first basibranchial+basihyal
                                                                                                      character.label
1 second basibranchial  present but reduced, posteriorly acuminate, and interlocked with first basibranchial+basihyal
                 study.label
1 Rosen and Greenwood (1976)

Entities:
    basibranchial 2 bone <http://purl.obolibrary.org/obo/UBERON_2001224>
Qualities:
    interlocked with <http://purl.obolibrary.org/obo/PATO_0002437>
Towards:
    basihyal bone <http://purl.obolibrary.org/obo/UBERON_0011618>
Exhibited by taxa:
                                          id                label
1 http://purl.obolibrary.org/obo/VTO_0071648    Monopterus boueti
2 http://purl.obolibrary.org/obo/VTO_0053650    Monopterus cuchia
3 http://purl.obolibrary.org/obo/VTO_0053654 Monopterus fossorius
4 http://purl.obolibrary.org/obo/VTO_0071645   Monopterus indicus

However, the /similarity/frequency endpoint fails to return any result for it (using the taxa corpus). @balhoff can you remind me why that is, and why that's expected? I assume the reason is that it is not propagated to any taxon profile?

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_0002437%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_2001224%253E%2529%250A%2B%2B%2B%2B%2Band%2B%2528%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002503%253E%2Bsome%2B%253Chttp%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0011618%253E%2529%2529%22%5D&corpus_graph=http%3A%2F%2Fkb.phenoscape.org%2Fsim%2Ftaxa" -H "accept: text/csv"
@hlapp hlapp added the question label Feb 15, 2020
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hlapp commented Feb 15, 2020

Also, if the count really should be zero, shouldn't the value retuned be zero, not nothing?

@hlapp hlapp added the bug label Feb 15, 2020
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hlapp commented Feb 16, 2020

The same problem occurs for the following phenotype, which at least appears to have a more complex taxon distribution:

> phens[16,"id"]
[1] "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_0002279%3E%0A+++++and+%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0000052%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0011618%3E%29%0A+++++and+%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002503%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_2001223%3E%29%29"
> as.phenotype(phens[16,"id"])
Phenotype 'basihyal bone tightly articulated with basibranchial 1 bone'
Linked to states:
                                        label
1 basihyal ankylosed with first basibranchial
                              character.label                study.label
1 basihyal ankylosed with first basibranchial Rosen and Greenwood (1976)

Entities:
    basihyal bone <http://purl.obolibrary.org/obo/UBERON_0011618>
Qualities:
    tightly articulated with <http://purl.obolibrary.org/obo/PATO_0002279>
Towards:
    basibranchial 1 bone <http://purl.obolibrary.org/obo/UBERON_2001223>
> as.phenotype(phens[16,"id"], withTaxa = TRUE)$taxa
                                           id                    label
1  http://purl.obolibrary.org/obo/VTO_0071642      Macrotrema caligans
2  http://purl.obolibrary.org/obo/VTO_0053649         Monopterus albus
3  http://purl.obolibrary.org/obo/VTO_0071648        Monopterus boueti
4  http://purl.obolibrary.org/obo/VTO_0053650        Monopterus cuchia
5  http://purl.obolibrary.org/obo/VTO_0071650        Monopterus eapeni
6  http://purl.obolibrary.org/obo/VTO_0053654     Monopterus fossorius
7  http://purl.obolibrary.org/obo/VTO_0071645       Monopterus indicus
8  http://purl.obolibrary.org/obo/VTO_0053645 Ophisternon aenigmaticum
9  http://purl.obolibrary.org/obo/VTO_0071653        Ophisternon afrum
10 http://purl.obolibrary.org/obo/VTO_0053646   Ophisternon bengalense
11 http://purl.obolibrary.org/obo/VTO_0071654     Ophisternon candidum
12 http://purl.obolibrary.org/obo/VTO_0071655    Ophisternon gutturale
13 http://purl.obolibrary.org/obo/VTO_0071652    Ophisternon infernale
14 http://purl.obolibrary.org/obo/VTO_0071657     Synbranchus madeirae
15 http://purl.obolibrary.org/obo/VTO_0053643   Synbranchus marmoratus

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.

@balhoff balhoff self-assigned this Mar 26, 2020
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