-
Dependencies on intake form seem incomplete -- OBI, Uberon?
-
treatment of 'history' is weird. BFO history (process) is imported but unreferenced. "smoking history" is defined as a "quality" but not as a subclass of "medical history".
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{ | |
"pre_mapped": { | |
"id": "ga4gh:VA.FLe4-pSUs7vjdVtVD4TmUNL4JhrBbqTd", | |
"type": "Allele", | |
"extensions": [ | |
{ | |
"name": "vrs_ref_allele_seq", | |
"value": "Y" | |
} | |
], |
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{ | |
"schemaVersion": 1, | |
"label": "QC", | |
"message": "N/A", | |
"color": "white", | |
"logoSvg": "<svg id=\"Layer_1\" data-name=\"Layer 1\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 135.54 133.3\"><defs><style>.cls-1{fill:#fff;}.cls-2{fill:#231f20;}</style></defs><path class=\"cls-1\" d=\"M85.31,20.58l-4-16.64s0,0,0,0c-1.11-.14-2.21-.26-3.33-.35s-2.24-.15-3.36-.18-2.26,0-3.4,0c-.82,0-1.66.06-2.49.11L63.21,19.66c-.22,0-.43.11-.65.15l0,.11c-1.58.3-3.13.68-4.65,1.12s-3,1-4.45,1.53L40.52,11.64c-.58.32-1.17.63-1.74,1-1,.56-1.91,1.14-2.83,1.74s-1.84,1.23-2.73,1.88-1.77,1.31-2.63,2l-.73.6L34.72,35c-.15.16-.28.33-.42.48v0c-1.12,1.18-2.17,2.42-3.17,3.7s-1.95,2.59-2.84,4h-.06v0l-16.83-1c-.31.62-.62,1.23-.91,1.85-.46,1-.88,2-1.29,3.07-.28.69-.53,1.39-.79,2.09-.12.35-.26.7-.38,1.05-.36,1-.69,2.1-1,3.17-.1.33-.17.68-.26,1l13.4,10.13a54.29,54.29,0,0,0-.56,10.73L5.25,84.54c.09.52.16,1,.26,1.55.21,1.08.44,2.16.7,3.23s.54,2.14.85,3.2.65,2.12,1,3.16c.14.42.31.82.46,1.24h0L25.22,97l0,0h.13a51.6,51.6,0,0,0,5.88,9 |
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{ | |
"oboscore": { | |
"dashboard_score_max_impact": { | |
"dashboard": 1, | |
"impact": 1, | |
"impact_external": 3, | |
"no_base": 5, | |
"overall_error": 20, | |
"overall_info": 5, | |
"overall_warning": 10, |
Each kind of response is slightly different, but this tries to make them more consistent in a few ways:
- No more gene vs normalized gene object. Everything is a GA4GH core
Gene
. This means no moreassociated_with
vsxref
, so one less kind ofMatchType
. - The outermost level includes the query, additional parameters passed to the API endpoint (I think (...?) this is good practice to include) and service information
- The outermost level also includes a
match
key that points to what the individual PythonQueryHandler
methods would return. IMO it makes more sense to move this stuff into the REST API response because these are things that you don't otherwise typically include in Python-to-Python methods (e.g. another class doesn't need to know what version of Gene Normalizer is running, it's literally sharing the environment). match
objects include source metadata and warnings. In some of the responses, we have previously included source metadata closer to the actual source matches, b
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[ issue-132-tests ⚙ venv] ~/code/fusor % ipython | |
Python 3.11.0 (main, Sep 6 2023, 12:48:52) [Clang 14.0.3 (clang-1403.0.22.14.1)] | |
Type 'copyright', 'credits' or 'license' for more information | |
IPython 8.16.1 -- An enhanced Interactive Python. Type '?' for help. | |
In [1]: from gene.database import create_db | |
In [2]: db = create_db() | |
In [3]: db.get_source_metadata("NCBI") |
We can make this file beautiful and searchable if this error is corrected: Unclosed quoted field in line 2.
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normalized_id normalized_xrefs normalized_strand normalized_hgnc_types normalized_ensembl_types normalized_ncbi_types normalized_hgnc_locations normalized_ensembl_locations normalized_ncbi_locations incoming_concept_id incoming_strand incoming_locations incoming_gene_type | |
hgnc:30046 ['ensembl:ENSG00000254093', 'ensembl:ENSG00000258724', 'ncbigene:54984'] - ['gene with protein product'] ['protein_coding'] [{'type': 'ChromosomeLocation', 'species_id': 'taxonomy:9606', 'chr': '8', 'start': 'p23.1', 'end': 'p23.1'}] [{'type': 'SequenceLocation', 'start': 10725398, 'end': 10839847, 'sequence_id': 'ga4gh:SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs'}] ncbigene:54984 + "[{""type"": ""ChromosomeLocation"", ""species_id"": ""taxonomy:9606"", ""chr"": ""8"", ""start"": ""p23.1"", ""end"": ""p23.1""}, {""type"": ""SequenceLocation"", ""start"": 10764960, ""end"": 10839875, ""sequence_id"": ""ga4gh:SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs""}, {""type"": ""SequenceLocation"", ""start"": 2507387, ""end"": 2582240, ""sequence_id"": ""g |
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('ncbigene:100131223', {'src_name': 'NCBI', 'concept_id': 'ncbigene:100131223', 'symbol': 'LOC100131223', 'strand': '-', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 28120833, 'end': 28121467, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO'}], 'label_and_type': 'ncbigene:100131223##identity', 'item_type': 'identity'}) | |
('ncbigene:440585', {'src_name': 'NCBI', 'xrefs': ['hgnc:34347'], 'concept_id': 'ncbigene:440585', 'symbol': 'FAM183A', 'strand': '+', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 43142961, 'end': 43156396, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO'}], 'label_and_type': 'ncbigene:440585##identity', 'item_type': 'identity'}) | |
('ncbigene:51668', {'src_name': 'NCBI', 'xrefs': ['hgnc:25019'], 'concept_id': 'ncbigene:51668', 'symbol': 'HSPB11', 'strand': '-', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 53911575, 'end': 53946305, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDe |
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(gene-normalization) ~/code/gene-normalization (issue-112) % ipython | |
Python 3.9.12 (main, Mar 26 2022, 15:51:15) | |
Type 'copyright', 'credits' or 'license' for more information | |
IPython 8.2.0 -- An enhanced Interactive Python. Type '?' for help. | |
In [2]: import boto3 | |
In [3]: g = boto3.resource("dynamodb").Table("gene_concepts") | |
In [4]: from boto3.dynamodb.conditions import Key |
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