Andrew Su

Unicode/string parsing error

5

I'm trying to parse structured metadata from [this url](https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/G4TBLF). I first executed this code on the example URL https://www.optimizesmart.com/how-to-use-open-graph-protocol/: ``` import extruct import requests from w3lib.html import get_base_url def extract_metadata(url):...

Hypothetical modeling of specific pharmacological modes of action

6

Naive question here... In the context of Translator, it seems likely that we will eventually want to model some detailed pharmacological modes of action, e.g., "antagonist" vs "inverse agonist". As...

create a "reference URL" (or similar) as a child of "association slot"

5

for capturing provenance that does not fit into the "publication" slot, for example

organize association_slot children

4

`association_slot` currently has the following children: - association type - association➞id - change is catalyzed by - clinical modifier qualifier - edge label - frequency qualifier - has confidence level...

Prompted by https://github.com/reusabledata/reusabledata/issues/50, we should review ways to make the existence of `_license` information in the JSON more clear. As two ideas, we could make specific note of the fact...

This paper https://www.sciencedirect.com/science/article/pii/S0002929718300624 describes another PheWAS study (similar to the one loaded in #66). Data are in Table S2 -- 1118 associations between SNV/SNPs and ICD-9 codes. This can probably...

More info: https://github.com/SuLab/GeneWikiCentral/issues/117

load VICC-harmonized data

1

From Alex Wagner, this link https://s3-us-west-2.amazonaws.com/g2p-0.10/index.html has the current release of the VICC-harmonized data (described in https://www.biorxiv.org/content/early/2018/07/11/366856). It is subject to change as that manuscript goes through peer review. But...

Matt Wright and Jimmy Zhen from the ClinGen team seemed interested in this idea at the CIViC hackathon. Need to reach out to them for more info on logistics...

Suggested by Beth Pitel (I think) at the CIViC Hackathon... I think the data is in this file http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/