Problems from the main tool
Terms which were not found with Lucene search. It might be possible to tweak search or add special weighting to improve search relevance. This needs to happen before the release of the curation tool. We need to check that all "high level/ commonly used terms are easily located.
New Lucene search issues
| search term | trying to locate | synonym type | notes |
Fixed Lucene search issues
| search term | trying to locate | synonym type | notes |
| flocculation | FYPO:0000155 | - | I see only, normal flocculation, absent flocculation (synonym)flocculating cell, I dont see synonym "increased flocculation" EXACT |
| splicing | GO:0000398 nuclear mRNA splicing, via spliceosome | 6 synonyms have sub-string splicing | maybe this term could have a name which made it clearer what it referred to? |
| protein binding | GO:0005515 | GO:0005515 does not come up as a first hit when searching for "protein binding" (had to search on the GO ID) | |
| plasma membrane | GO:0005886 | 'plasma membrane part' show on top. And then children thereof. 'Plasma membrane' doesn't show at all | |
| G2/M | - | - | no results although lots visible at G2 |
| lysis | cell lysis (phenotype) | cytolysis | when searching for lysis, cytolysis comes up, which is the synonym of cell lysis, which is what I was looking for. I thought it was odd that the synonym shows and not the primary name although the primary has the same term in it. SourceForge item |
| regulation of transcription from RNA polymerase II promoter | does not locate "regulation of transcription from RNA polymerase II promoter" as a top hit | term name | oddly transcription from RNA polymerase II promoter does |
| nucleate | mononucleate (FYPO:60), binucleate (FYPO:1222), multinucleate (FYPO:61) and descendants | just 'nucleate' finds nothing, but seems it should find 9 terms by name + one by synonym | |
- Synonyms
I suspect exact match (rather than sub-string) to broad, related or exact should be equally high (more relevant)
i.e "transcription" is "broad" for transcription, DNA dependent "splicing" is a ? synonym for nuclear mRNA cis splicing, via spliceosome we should extend this list of synonym test cases where we think a biologist will intuitively search for a term which is not the primary term name to test how well it works (at the moment neither of the correct terms in these cases have very high relevance, however the splicing synonym hasn't yet been added...when it has we should tweak the relevance and test), in the meantime any other "test" terms would be useful...would also good to see if things get harder to find after the changes
