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This package handles the Open Targets data checking.

Project description

Check-O-Matic

Install

pip install opentargets-checkomatic
opentargets_checkomatic eval -f platform-api.yml

The YAML file can be like this

checkomatic:
  client:
    host: https://platform-api.opentargets.io
    port: 443
    size: 100 # max size to fetch when query and it is applicable
  rules:
    targets:
      DMD:
        - |-
          # print('target approved name', o.approved_name)
          output = True
        - o['id'] == 'ENSG00000198947'
    diseases:
      Orphanet_908:
        - o.name == 'Fragile X syndrome'
        - o.association_counts.total > 400
        - o.association_counts.direct > 400
      Orphanet_273:
        - o.name == 'Steinert myotonic dystrophy'
      Orphanet_93256:
        - o.name == 'Fragile X-associated tremor/ataxia syndrome'
    associations:
      # these (targets and diseases) use dataframes (t) instead addict.Dict object (o)
      # those are easier to manipulate and filter by
      targets:
        PRDX1:
        DMD:
          - ('Orphanet_98896' in to_vlist(jp.parse('data[*].disease.id').find(d)))
        CD86:
          - ('EFO_0003885' in to_vlist(jp.parse('data[*].disease.id').find(d)))
        ITGAL:
          - ('EFO_0003767' in to_vlist(jp.parse('data[*].disease.id').find(d)))
      diseases:
        Orphanet_93256:
        EFO_0003767:
          # NOD2, IL10RA, IL23R, ITGAL in IBD
          - not set(['NOD2', 'IL10RA', 'ITGAL']) - to_vset(jp.parse('data[*].target.gene_info.symbol').find(d))
        EFO_0000384:
          # TNF, PTGS2, PTGS1 in crohns disease
          - not set(['TNF', 'PTGS2', 'PTGS1']) - to_vset(jp.parse('data[*].target.gene_info.symbol').find(d))
        EFO_0000249:
          # APP, SORL1, ABCA7, ADAM10 in alzheimers disease
          - not set(['APP', 'SORL1', 'ABCA7', 'ADAM10']) - to_vset(jp.parse('data[*].target.gene_info.symbol').find(d))
        Orphanet_399:
          # huntington disease
          - not set(['HTT']) - to_vset(jp.parse('data[*].target.gene_info.symbol').find(d))
    evidences:
      # these (evidences) use dataframes (t) instead addict.Dict object (o)
      # those are easier to manipulate and filter by
      # check for Should have literature, drugs, animal models and
      # at least 1 piece of genetic evidence (i.e. trinucleotide expansions from ClinVar) for HTT.
      ENSG00000102081-Orphanet_908:
        # http://purl.obolibrary.org/obo/SO_0001583
        - ('missense_variant' in to_vlist(jp.parse('data[*].evidence.evidence_codes_info[*][*].label').find(d)))
    searches:
      diseases:
        "crohn disease":
          - len(o.data) > 0
      targets:
        "mt-nd":
          - len(o.data) > 0
    stats:
      - o.data_version == "18.12"
      - o.targets.total > 28000 and o.targets.total < 50000
      - o.diseases.total > 10000 and o.diseases.total < 20000
      - len(o.associations.datatypes.keys()) == 7
      - ('sysbio' in o.associations.datatypes.affected_pathway.datasources)
      - |-
        dts = o.associations.datatypes.keys()
        dss = []
        for dt in dts:
          dss += o.associations.datatypes[dt].datasources.keys()
        output = len(dss) == 19

Copyright

Copyright 2014-2018 Biogen, Celgene Corporation, EMBL - European Bioinformatics Institute, GlaxoSmithKline, Takeda Pharmaceutical Company and Wellcome Sanger Institute

This software was developed as part of the Open Targets project. For more information please see: http://www.opentargets.org

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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