meringlab/paxdb-api

abundance microservice

paxdb-api's Issues

return 4xx or 3xx if dataset exists but doesn't belong to the specified species

incorrect url, but returns 200 ok: http://imlslnx-titan.uzh.ch:13000/dataset/4932/1
correct url: http://imlslnx-titan.uzh.ch:13000/dataset/7227/1

bug: correlation between 4932 and 882

dataset correlation

needs to sum orthgroup abundances, and for that needs to know about the phylo tree.

missing abundance value/wrong rank

api call returns:

{
  "id": 1854304,
  "externalId": "9606.ENSP00000355124",
  "name": "KRT19",
  "annotation": "Keratin 19; Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle",
  "hasFamily": true,
  "uniprotId": "P08727",
  "abundances": [
    {
      "datasetInfo": {
        "id": 99,
        "name": "H.sapiens - Cell line, A431 (Lundberg,MSB,2010)",
        "score": 7.86,
        "weight": "100%",
        "description": "abundance based on MAPPED_BY_AUTHORS, A431, from<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/21179022\" target=\"_blank\">lundberg,MSB,2010</a><br/><b>Interaction consistency score</b>: 7.86&nbsp<b>Coverage</b>: 24",
        "organ": "CELL_LINE",
        "integrated": false,
        "coverage": 24,
        "publication_year": 2010,
        "num_abundances": 5388,
        "hasPeptideCounts": false,
        "filename": "9606-A431_cellline_Lundberg_2010.txt"
      },
      "formattedAbundance": "NA",
      "rank": "1. out of 5388 [top 5%]"
    },

how can rank be 1st but abundance missing!?

histogram: smaller images