mzabriskie

If you're like me you have a dir like ~/Workspace/Github where all your git repos live. I often find myself making a change in a repo, getting side tracked and ending up in another repo, or off doing something else all together. After a while I end up with several repos with modifications. This script helps me pick up where I left off by checking the status of all my repos, instead of having to check each one individually.

Usage:

git-status [directory]

This will run git status on each repo under the directory specified. If called with no directory provided it will default to the current directory.

balhoff

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Term1: <http://purl.obolibrary.org/obo/PATO_0000587>
PREFIX Term2: <http://purl.obolibrary.org/obo/PATO_0000586>
SELECT ?nearest
FROM <http://purl.obolibrary.org/obo/pato.owl>
WHERE {
	Term1: rdfs:subClassOf* ?nearest .
	Term2: rdfs:subClassOf* ?nearest .
	Term1: rdfs:subClassOf* ?indirect .
	Term2: rdfs:subClassOf* ?indirect .

joelkuiper

tui,label
T001,Organism
T002,Plant
T004,Fungus
T005,Virus
T007,Bacterium
T008,Animal
T010,Vertebrate
T011,Amphibian
T012,Bird

urbanecm

#!/usr/bin/env python
#-*- coding: utf-8 -*-

import pywikibot
import json

CLAIMS = ['Q41197-3527CCB4-A422-4B31-AED4-BB2CCBF07790']
NEW_RANK = 'deprecated'
SUMMARY = 'Deprecating %s' # %s will be replaced with claim ID

tkuhn

Welcome to the New Era of Scientific Publishing

— by Tobias Kuhn, 4 April 2022; reporting on work with Cristina Bucur, Davide Ceolin, and Jacco van Ossenbruggen [1,2] —

I believe we have made the first steps venturing into a new era of scientific publishing. Let me explain. [Update: At what point exactly a new era begins and what counts as first steps are of course subject to debate. I therefore added a section on related initiatives and further reading below.]

Science is nowadays communicated in a digital manner through the internet. We essentially have a kind of "scientific knowledge cloud", where researchers with the help of publishers upload their latest findings in the form of scientific articles, and where everybody who is interested can access and retrieve these findings. (This is in fact only true for articles that are published as Open Access, but that is not the point here.)

cthoyt

import bioregistry


def main():
    """Identify resources with uncurated bananas."""
    for resource in bioregistry.resources():
        pattern = resource.get_pattern()
        if not pattern:
            continue
        for peel in ":_-":

cmungall

Using OAK to retrieve definitions

For more OAK examples, see

• https://incatools.github.io/ontology-access-kit/notebooks.html

Setup

$ pip install oaklib