Chunlei Wu
Chunlei Wu
Currently, BioThings API's annotation endpoint supports query by supported ID directly, e.g. in MyGene.info API: ``` GET /v3/gene/1017 POST /v3/gene ids: 1017,1018 ``` After the fix of #305, we can...
`utils.dataload.dict_sweep` is used to: >Remove keys whose values are ".", "-", "", "NA", "none", " "; and remove empty dictionaries It's quite powerful, but could be potentially dangerous to remove...
Difference between `query` and `filter` context in an ES query: https://www.elastic.co/guide/en/elasticsearch/reference/current/query-filter-context.html The query placed in the `filter` context can be faster than in the normal `query` context (e.g. passed to...
Elasticsearch snapshot supports lifecycle management policy (SLM), we can set a policy like this: ``` "retention": { "expire_after": "30d", "min_count": 5, "max_count": 50 } ``` Let's add it to hub...
[Poetry](https://python-poetry.org) seems to be gaining popularity in Python world. We can consider switching to it. It can replace the current `setup.py` and/or `requirements*.txt` files. Poetry works similarly to `npm` for...
with MongoKit v0.7.2: ``` structure={'foo': OR(unicode,int)} ``` works, but this won't work: ``` structure={'foo': OR(unicode,[unicode])} ``` I have a use case that a field can be either a string (if...
With the latest biothings sdk release (0.12.4+), we can now add the CURIE ID support for MyVariant API: We currently have these in the `config_web.py`: ``` ANNOTATION_ID_REGEX_LIST = [ (re.compile(r'rs[0-9]+',...
URL: https://gsrs.ncats.nih.gov It provides a downloadable `.gsrs` file. And this file is essentially a compressed 7-zip file with a list of JSON objects. NOTE: GSRS resource is likely a successor...
As shown in this example: https://mychem.info/v1/query?q=bromazin&fields=pharmgkb * **generic_names** & **trade_names** fields should be a list * **dosing_guideline**: check if it can be a True/False boolean field * fields under **xrefs**...
UNII data source dumper is here: https://github.com/biothings/mychem.info/blob/master/src/hub/dataload/sources/unii/unii_dump.py and from @andrewsu: > looks like that dumper gets the `UNII_Data.zip` file on that page. In addition `UNIIs.zip` could be useful. For example,...