Biopragmatics

The International Society of Biocuration (ISB) partners with the journal Database to get discounts for its members when they publish there.

The Open Researcher and Contributor Identifier (ORCID) database is an invaluable resource that supports the unambiguous identification of researchers.

I’ve just returned from the 17th Annual International Biocuration Conference at the Indian Biological Data Centre (IBDC) in Faridabad, India.

Using Pydantic for encoding data models and FastAPI for implementing APIs on top of them has become a staple for many Python programmers.

I finally got back into reading!

The Unified Medical Language System (UMLS) is a widely used biomedical and clinical vocabulary maintained by the United States National Library of Medicine.

I’ve been working on improving reproducibility in the field of cheminformatics for some time now.

Today’s short post is about three SPARQL queries I wrote to get bibliometric information about journals and publishers out of Wikidata.

I was recently nominated for the International Society for Biocuration’s Excellence in Biocuration Early Career Award (results will be announced on June 14th!).

Archival Resource Keys (ARKs) are flavor of persistent identifiers like DOIs, URNs, and Handles that have the benefit of being free, flexible with what metadata gets attached, and natively able to resolve to web pages.

This blog is normally about very serious science, but I’m taking a break from that for the evening to advertize my band’s upcoming show on April 8th in the SPH Music Masters Finale (aka, the German Battle of the Bands).

Several controlled vocabularies and ontologies that aren’t themselves OBO Foundry ontologies use unsanctioned OBO PURLs.

This post gives a brief background on the formal definition of the syntax and semantics of compact uniform resource identifiers (CURIEs) from the Worldwide Web Consortium (W3C) and investigates how many prefixes in the Bioregistry are compliant with the s…

The semantic web and ontology communities needed a reusable Python package for converting between uniform resource identifiers (URIs) and compact URIs (CURIEs) that is reliable, idiomatic, generic, and performant.

Way back in 2021, during the annual general assembly of the International Society for Biocuration (ISB) at the 14th Annual International Biocuration Conference (Biocuration 2021) , there was a discussion about the notably underutilized budget of the socie…

The 16th Annual International Biocuration Conference (Biocuration 2023) is taking place in Padua, Italy from April 24-26th, 2023.

After the BioCypher preprint went up on the arXiv, I checked in on the missing co-author items list on the Scholia page that reflects my Wikidata entry.

The Global Biodata Coalition released a list of Global Core Biodata Resources (GCBRs) in December 2022, comprising 37 life science databases that they considered as having significant importance (selected following this procedure).

There has been legitimate concern about the future of Twitter over the last week due to its new ownership and management.

This blog post is a tutorial on how to curate the links between a researcher and scholarly works (e.g., pre-prints, publications, presentations) on Wikidata using Scholia and the Author Disambiguator tool.

While we were recently preparing to submit a manuscript, the lead author said they looked at my last few papers and noticed I always used a private email address instead of an institutional email address.

As a follow-up to my previous post on refactoring and improving a machine learning model implemented with PyTorch, this post will be a tutorial on how to generalize the implementation of a multilayer perceptron (MLP) to use one of several potential non-li…

This blog post is a tutorial that will take you from a naive implementation of a multilayer perceptron (MLP) in PyTorch to an enlightened implementation that simultaneously leverages the power of PyTorch, Python’s built-ins, and some powerful third party…

I figured over the holiday break or early days of the new year, I’d catch up on some serious blogging.

After the recent incident on the OBO Foundry where an inexperienced group submitted a new ontology request using a prefix that already existed in the BioPortal, there has been a renewed interest in implementing an automated solution to protect against thi…

There are a lot of terms that I’ve been throwing around when talking about the Bioregistry, so this blog post is a first draft of a gloassary of all of them.

With the recent paper on Gilda and approaching INDRA 2 and INDRA database papers coming up, I’ve put together a visual guide on how to curate statements extracted by INDRA through the web interface at https://db.indra.bio.

Compact uniform resource identifiers, or CURIEs, are an important formalism for referencing biomedical entities.

This post is about my personal code style guide that are beyond the enforcement of my flake8 plugins or black.

PostgreSQL is a powerful relational database management system that can be easily downloaded and installed from its official image on DockerHub using Docker.

I’ve spent the last two days cleaning up some research machine learning code that blew up when I tried applying it to my own data due to memory constraints.

In a previous post, I described how to formalize the information about a research organization using Wikidata.

In his blog post, Some Thoughts on Comparing Classification Models, Pat Walters illustrated enlightened ways to convey the results of training and evaluating machine learning models on hERG activity data from ChEMBL (spoiler: it includes box plots).

ChEMBL is easily the most useful database in a cheminformatician’s toolbox, containing structural and activity information for millions of diverse compounds.

This is a more personal blog post about my experience as an american expat in Germany - specifically about my experiences at the Bonner Ausländeramt (Bonn’s Foreigner’s Office of the City of Bonn).

The mean rank (MR) and mean reciprocal rank (MRR) are among the most popular metrics reported for the evaluation of knowledge graph embedding models in the link prediction task.

After many discussions scientists from AstraZeneca’s knowledge graph and target prioritization platform (BIKG) about the PyKEEN knowledge graph embedding model package, I joined them in writing a review on biomedical knowledge graphs.

In late 2017, I visited the Critical Path Institute in Tucson, Arizona with my colleague Daniel Domingo-Fernández to use our Alzheimer’s disease map encoded in the Biological Expression Language (BEL) and the tools we built with PyBEL to help contextualize

Writing excellent documentation is crucial for open source software projects.

Scholia is a powerful frontend for summarizing authors, publications, institutions, topics, etc. that draws content from Wikidata.

If you’ve ever read a scientific paper, you know that the information that makes it into the author affiliations is a mess.

Previous posts in my “How to Code with Me” series have addressed packaging Python code and setting up a command line interface (CLI) using click.

Domingo-Fernandez et al. published ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases. in 2018 describing the overlap between human pathways in KEGG, Reactome, and WikiPathways.

If you’re reading my blog, there’s a pretty high chance you’ve used DrugBank, a database of drug-target interactions, drug-drug interactions, and other high-granularity information about clinically-studied chemicals.

When training a knowledge graph embedding model with inverse triples, two scores are learned for every triple (h, r, t) - one for the original and one for the inverse triple (t, r', h).

PyKEEN has a wide variety of functionality related to knowledge graph embedding models and handling various sources of knowledge graphs.

Many of the proteins in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are cleavage products of the replicase polyprotein 1ab (uniprot:P0DTD1).

One of the cardinal sins in computational science is to hard code a file path in your analysis.

While I led the curation program in the Human Brain Pharmacome project during my Ph.D. from 2018-2019 at Fraunhofer, we built the Curation of Neurodegeneration Supporting Ontology (CONSO).

This blog post is the next installment in the series about all of the very particular ways I do software development in Python.