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uniprot / enzymeportal

The EBI Enzyme Portal
http://www.ebi.ac.uk/enzymeportal/
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No Result found for 17-BETA HYDROXYSTEROID DEHYDROGENASE III DEFICIENCY #177

Closed computingfacts closed 10 years ago

computingfacts commented 10 years ago

when searching for 17-BETA HYDROXYSTEROID DEHYDROGENASE III DEFICIENCY, no result is found. however, if you search EBI website, it returns some results. could this be a problem at Enzyme Portal? needs to investigate and possibly fix ASAP.

same thing also applied to "breast neoplasm"

computingfacts commented 10 years ago

This problem could be the same reason why when you search for "acatalasia", no result is returned. but debugging Ep source file shows that one result was found but later lost. currently investigating the method call to uniprot webservice (Uniprot Adapter) from Ep core

rafael-alcantara commented 10 years ago

Currently we search the following domains in EB-Eye: uniprot, chebi, intenz, rhea, reactome, chembl-compound, pdbe. Diseases domains - omim, mesh, efo - are missing from our search, so it should be just a matter of adding them.

rafael-alcantara commented 10 years ago

I have added those three domains to ebeye-adapter-1.0.4, and fixed some wrong queries to EB-Eye (generic searches to uniprot domain when they were supposed to be field-specific).

All is fixed in ep-core-1.0.20, now being used in ep-web-client-1.0.25-SNAPSHOT.

I made some tests to compare the current version (1.0.24) and the fixed one (1.0.25-SNAPSHOT)(current > fixed):

Search_term  Response_(s) Num._of_Results SpeciesFilters CompoundFilters DiseaseFilters
sildenafil   2 > 5        20 > 20         11 > 11        39 > 39         3 > 3
CFTR         17 > 3       18 > 3          121 > 74       36 > 9          3 > 1
REACT_1400.4 8 > 7        3 > 3           19 > 19        3 > 3           0 > 0
Q13423       4 > 1        1 > 1           3 > 3          4 > 4           0 > 0
acatalasia   0 > 2        0 > 1           0 > 112        0 > 13          0 > 2
alzheimer    68 > 10      26 > 12         221 > 249      71 > 58         25 > 14
17-BETA...   0 > 1        0 > 1           0 > 3          0 > 5           0 > 2

Response times are typical and approximate. Note that we now get results for disease names ('acatalasia', '17-beta hydroxysteroid dehydrogenase III deficiency') In some cases ('CFTR', 'alzheimer') the number of results decreases as a consequence of using selected fields for searching uniprot domain, instead of searching all of its index. This makes the result list shorter and more accurate. In the case of 'alzheimer', the response time is decreased to a manageable level (more than 30 s triggers the load balancer timeout which results in an error for the end user). As expected, the number of filters only depends on the final number of results.