Daniel Himmelstein

For new mansucript setup, see https://github.com/greenelab/manubot-rootstock/blob/master/SETUP.md. Windows users, try [Git Bash](https://git-for-windows.github.io/) to enter to commands.

> Is it possible to do this remotely another time please? Certainly! It's always possible, and we're trying to document the setup process, so most users won't need any in-person...

# 2018 OpenCon Update I won't be at OpenCon 2018 sadly, but attendees should feel free to contribute or experiment with Manubot as part of the Do-A-Thon. For some more...

+1 to using CURIEs as per identifiers.org for xref prefixes. Noting https://github.com/EBISPOT/efo/issues/878 regarding EFO xref prefixes.

Are you referring to the following in [`SIDER4.ipynb`](https://github.com/dhimmel/SIDER4/blob/be3adebc0d845baaddb907a880890cb5e85f5801/SIDER4.ipynb): ```python # Read DrugBank terms url = 'https://raw.githubusercontent.com/dhimmel/drugbank/3e87872db5fca5ac427ce27464ab945c0ceb4ec6/data/drugbank.tsv' drugbank_df = pandas.read_table(url)[['drugbank_id', 'name']].rename(columns={'name': 'drugbank_name'}) # Pubchem to DrugBank mapping url = 'https://raw.githubusercontent.com/dhimmel/drugbank/3e87872db5fca5ac427ce27464ab945c0ceb4ec6/data/mapping/pubchem.tsv' drugbank_map_df...

Data from this repository is ingested by Hetionet v1.0 in [cells 53-56 of this notebook](https://github.com/dhimmel/integrate/blob/93feba1765fbcd76fd79e22f25121f5399629148/integrate.ipynb). The side effect terms from SIDER are inserted into Hetionet v1.0 via their UMLS identifiers....

Ah this is a real deal-breaker to an otherwise nice package! Although I am glad the package did show the following warning: ``` WARNING:eutils._internal.client:NCBI found 13241 results, but we truncated...

> Your published analyses only show these for specific journals. The table in the "Publication delays at PLOS and 3,475 other journals" [blog post](http://blog.dhimmel.com/plos-and-publishing-delays/#journals_wrapper) contains median time to acceptance and...

> I want an aggregate value of the mean times for all journals. Okay here's some Python code to get the mean acceptance and publication times across all articles: ```python...

> But I am not sure how the submission to acceptance time can be longer than the submission to publication time (since the latter includes the former)? My bad. 43.1...