Improve tagging of traits

[Arnold Kuzniar]

Previously, the query with days to fruit ripening returned QTL:4321030_4_1 in tomato but it's not found in the current data. The reason is that Days to 1st ripe fruit has not been tagged (i.e., with SP:0000366). It could be that previously this was done manually.

[Matthijs Brouwer]

To reproduce:

In qtl.csv, the output for Days to 1st ripe fruit returns

pmc_id,tab_lb,row_id,tab_id,trait_in_article,trait_in_onto,trait_uri,chromosome,marker,marker_uri,gene,gene_uri,doi
4321030,4,1,5,"Days to 1st ripe fruit",fruit,http://purl.obolibrary.org/obo/PO_0009001;http://purl.obolibrary.org/obo/SP_0000037,"",J1,http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene358_0-i2;http://solgenomics.net/genome/Solanum_pennellii/variation/cLES-5-J1,,,10.1534/g3.114.014654

Information for Days to 1st ripe fruit is received from a SOLR request, posting the lowercase version to the tag handler:

curl -s -H "Content-Type: text/plain" --data "days to 1st ripe fruit" -X POST "http://localhost:8983/solr/trait_descriptors/tag?fl=uuid,code,prefterm,term&overlaps=LONGEST_DOMINANT_RIGHT&matchText=true&tagsLimit=5000&wt=json"

resulting in

{
  "responseHeader": {
    "status": 0,
    "QTime": 1
  },
  "tagsCount": 1,
  "tags": [
    [
      "startOffset",
      17,
      "endOffset",
      22,
      "matchText",
      "fruit",
      "ids",
      [
        "397addd5-68cf-4a10-801f-828b9ec63ceb",
        "e3385271-2e1e-47d0-9ab0-6f540e2f13fe"
      ]
    ]
  ],
  "response": {
    "numFound": 2,
    "start": 0,
    "docs": [
      {
        "uuid": "397addd5-68cf-4a10-801f-828b9ec63ceb",
        "code": "http://purl.obolibrary.org/obo/PO_0009001",
        "term": "fruit",
        "prefterm": "fruit"
      },
      {
        "uuid": "e3385271-2e1e-47d0-9ab0-6f540e2f13fe",
        "code": "http://purl.obolibrary.org/obo/SP_0000037",
        "term": "fruit",
        "prefterm": "fruit"
      }
    ]
  }
}

resulting in PO_0009001 and SP_0000037 as the found traits in the ontology...