Unraveling complex biology with biological knowledge graphs. Content licensed under CC BY 4.0.

Charles Tapley Hoyt

PEP 735 introduced dependency groups in packaging metadata, which are complementary to optional dependencies in that they might not correspond to features in the package, but rather be something like development or release dependencies. I am slowly working towards updating my cookiecutter template cookiecutter-snekpack to use PEP 735. So far, uv and tox have released support - all that’s left is ReadTheDocs.

Dependency Groups and ReadTheDocs

I’m working through making a contribution to pandoc that adds first-class support for author role annotations using the Contribution Role Taxonomy (CRediT) and also outputs compliant Journal Publishing Tag Set (JATS) XML. This has lead me down a (losing) journey with learning the Haskell programming language, so I thought I would post a short note on a function I tried to understand.

Some Haskell I Tried to Write

Graphviz is software for graph visualization written in C. PyGraphviz provides a nice Python wrapper for it. The issue is that getting Python to know about the C headers changes every few months. I’ll try and keep this blog post updated every time there are some changes.

Building Graphviz when installing PyGraphviz

Several controlled vocabularies and ontologies that aren’t themselves OBO Foundry ontologies use unsanctioned OBO PURLs. This post is about how to use the Bioregistry to identify which resources are doing this and to give some insight into how we arrived in this situation. Background on the OBO Foundry   The OBO Foundry is a set of independent, interoperable biomedical ontologies that aspire to using shared development principles.

Resources masquerading as OBO Foundry ontologies

Today’s short post is about three SPARQL queries I wrote to get bibliometric information about journals and publishers out of Wikidata. Each of the following queries can be readily copy-pasted into the Wikidata Query Service and run in the browser.

Querying Journals and Publishers in Wikidata

I’ve just returned from the 17

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Annual International Biocuration Conference at the Indian Biological Data Centre (IBDC) in Faridabad, India.

Discussions and Follow-ups from Biocuration 2024

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

Semantic Pydantic

I finally got back into reading! Over winter break 2022, I started the Stormlight Archive then followed up in 2023 by reading the entirety of Brandon Sanderson’s

 Cosmere

, as well as a some other fantasy, science fiction, and literary fiction. Here’s the list.

Books I Read in 2023

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. Name-to-Thing (N2T) implements a resolver for a variety of ARKs, so this blog post is about how that resolver can be re-implemented with the curies Python package. In a lot of ways, ARKs look and act like CURIEs.

Re-implementing the N2T ARK Resolver

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 8

 th

in the SPH Music Masters Finale (aka, the German Battle of the Bands). We need your support!

The Representatives of Monkey Jack - German Battle of the Bands Finale

Authorships are

The Open Researcher and Contributor Identifier (ORCID) database is an invaluable resource that supports the unambiguous identification of researchers. However, its first party data dump is too complex, verbose, and unstandardized for many use cases. This post describes open source software I wrote that automates downloading, processing, and exporting ORCID into a more usable form. I put the results on Zenodo under the CC0 license.

Easier ORCID

The International Society of Biocuration (ISB) partners with the journal Database to get discounts for its members when they publish there. This means the ISB’s executive committee needs to send a member list to the journal’s editor.

Programmatic Access to a Wordpress User List

The Unified Medical Language System (UMLS) is a widely used biomedical and clinical vocabulary maintained by the United States National Library of Medicine. However, it is notoriously difficult to access and work with due to licensing restrictions and its complex download system. In the same vein as my previous posts about DrugBank and ChEMBL, this post describes open source software I’ve developed for downloading and working with this data.

Unlocking UMLS

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

 th

!). This made me curious about how to model nominations and awards on Wikidata. In this post, I’ll describe how to curate awards, nominations, recipients, and how to make SPARQL queries to get them.

Modeling and Querying Awards in Wikidata

I’ve been working on improving reproducibility in the field of cheminformatics for some time now. For example, I’ve written posts about making data from DrugBank and ChEMBL more actionable. Over the last year, I’ve been preparing a concept with the editors of the Journal of Cheminformatics on how to include an assessment of reproducibility to reviews of manuscripts submitted to the journal.

Reproducibility Pilot in the Journal of Cheminformatics

Biopragmatics

Several controlled vocabularies and ontologies that aren't themselves
[OBO Foundry](https://obofoundry.org/) ontologies use unsanctioned OBO
PURLs. This post is about how to use [the
Bioregistry](https://bioregistry.io/) to identify which resources are
doing this and to give some insight into how we arrived in this
situation.

## Background on the OBO Foundry

The [OBO Foundry](https://obofoundry.org/) is a set of independent,
interoperable biomedical ontologies that aspire to using [shared
development
principles](https://obofoundry.org/principles/fp-000-summary.html). One
such principle is to use a principled approach for creating persistent
uniform resource locators (PURLs) for local unique identifiers in each
ontology. These PURLs follow the form
`http://purl.obolibrary.org/obo/_`{.language-plaintext
.highlighter-rouge}. For example, a prefix might be
`GO`{.language-plaintext .highlighter-rouge} (for the Gene Ontology) and
local unique identifier might be `0032571`{.language-plaintext
.highlighter-rouge} (for *response to vitamin K* in GO) resulting in the
PURL <http://purl.obolibrary.org/obo/GO_0032571>.

While most semantic web resources allow the use of any IRIs
(internationalized resource identifiers), the OBO Foundry enforces that
its PURLs resolve to something useful for readers (e.g., to the
[Ontology Lookup Service](https://www.ebi.ac.uk/ols)). The resolver
behind <http://purl.obolibrary.org> is implemented and maintained in a
[GitHub repository](https://github.com/OBOFoundry/purl.obolibrary.org/)
with corresponding `.htaccess`{.language-plaintext .highlighter-rouge}
files for each OBO Foundry ontology. Correct and useful configuration
for each ontology are a requirement for acceptance to the OBO Foundry.

At the core of the OBO Foundry are several high quality, well-known,
generally useful ontologies such as the [Gene
Ontology](https://bioregistry.io/go) and the [Cell
Ontology](https://bioregistry.io/go). Inclusion in the OBO Foundry has
therefore become a *de facto* stamp of approval for ontologies that
(until now) 254 ontologies have (for better or worse) successfully
sought out.

## The Masquerade

Unfortunately, some ontologies and controlled vocabularies have adopted
OBO PURLs even though they are not OBO Foundry ontologies. This is a
problem for a few reasons:

1. The PURLs are not registered in
 <https://github.com/OBOFoundry/purl.obolibrary.org/> and therefore
 do not resolve
2. The quality of the ontology has not been vetted, meaning that
 low-quality ontologies using OBO PURLs could damage community trust
 in the OBO Foundry
3. These PURLs might conflict with other URIs prefix synonyms,
 increasing complexity for data integration
4. Most importantly: it's confusing.

One of the jobs of [the Bioregistry](https://bioregistry.io/) is to
catalog the URI format strings for identifier resources useful for the
life and natural sciences. This allows us to assess how big the problem
of non-OBO Foundry ontologies are using OBO PURLs, and why. Without
further ado, here's the list of offending resources that appear in the
Bioregistry:

| prefix | name | evidence | uri_prefix |
|-----------------------------------------------------------|-------------------------------------------------|---------------|-------------------------------------------------------------------------------------|
| [aeon](https://bioregistry.io/aeon) | Academic Event Ontology | curated | `http://purl.obolibrary.org/obo/AEON_`{.language-plaintext .highlighter-rouge} |
| [cemo](https://bioregistry.io/cemo) | COVID-19 epidemiology and monitoring ontology | extra | `http://purl.obolibrary.org/obo/cemo.owl#`{.language-plaintext .highlighter-rouge} |
| [covoc](https://bioregistry.io/covoc) | CoVoc Coronavirus Vocabulary | curated | `http://purl.obolibrary.org/obo/COVOC_`{.language-plaintext .highlighter-rouge} |
| [decipher](https://bioregistry.io/decipher) | DECIPHER CNV Syndromes | biocontext | `http://purl.obolibrary.org/obo/DECIPHER_`{.language-plaintext .highlighter-rouge} |
| [dermo](https://bioregistry.io/dermo) | Human Dermatological Disease Ontology | curated | `http://purl.obolibrary.org/obo/DERMO_`{.language-plaintext .highlighter-rouge} |
| [efo](https://bioregistry.io/efo) | Experimental Factor Ontology | biocontext | `http://purl.obolibrary.org/obo/EFO_`{.language-plaintext .highlighter-rouge} |
| [gorel](https://bioregistry.io/gorel) | GO Relations | biolink | `http://purl.obolibrary.org/obo/GOREL_`{.language-plaintext .highlighter-rouge} |
| [hpath](https://bioregistry.io/hpath) | Histopathology Ontology | curated | `http://purl.obolibrary.org/obo/MC_`{.language-plaintext .highlighter-rouge} |
| [idocovid19](https://bioregistry.io/idocovid19) | COVID-19 Infectious Disease Ontology | curated | `http://purl.obolibrary.org/obo/COVIDO_`{.language-plaintext .highlighter-rouge} |
| [lbo](https://bioregistry.io/lbo) | Livestock Breed Ontology | curated | `http://purl.obolibrary.org/obo/LBO_`{.language-plaintext .highlighter-rouge} |
| [lpt](https://bioregistry.io/lpt) | Livestock Product Trait Ontology | curated | `http://purl.obolibrary.org/obo/LPT_`{.language-plaintext .highlighter-rouge} |
| [mesh](https://bioregistry.io/mesh) | Medical Subject Headings | biocontext | `http://purl.obolibrary.org/obo/MESH_`{.language-plaintext .highlighter-rouge} |
| [msio](https://bioregistry.io/msio) | Metabolomics Standards Initiative Ontology | curated | `http://purl.obolibrary.org/obo/MSIO_`{.language-plaintext .highlighter-rouge} |
| [omia](https://bioregistry.io/omia) | Online Mendelian Inheritance in Animals | biocontext | `http://purl.obolibrary.org/obo/OMIA_`{.language-plaintext .highlighter-rouge} |
| [omim](https://bioregistry.io/omim) | Online Mendelian Inheritance in Man | biocontext | `http://purl.obolibrary.org/obo/OMIM_`{.language-plaintext .highlighter-rouge} |
| [pride](https://bioregistry.io/pride) | PRIDE Controlled Vocabulary | curated | `http://purl.obolibrary.org/obo/PRIDE_`{.language-plaintext .highlighter-rouge} |
| [reo](https://bioregistry.io/reo) | Reagent Ontology | curated | `http://purl.obolibrary.org/obo/REO_`{.language-plaintext .highlighter-rouge} |
| [roleo](https://bioregistry.io/roleo) | Role Ontology | curated | `http://purl.obolibrary.org/obo/RoleO_`{.language-plaintext .highlighter-rouge} |
| [soybase](https://bioregistry.io/soybase) | SoyBase | prefixcommons | `http://purl.obolibrary.org/obo/`{.language-plaintext .highlighter-rouge} |
| [uniprot.isoform](https://bioregistry.io/uniprot.isoform) | UniProt Isoform | extra | `http://purl.obolibrary.org/obo/UniProtKB_`{.language-plaintext .highlighter-rouge} |
| [vido](https://bioregistry.io/vido) | Virus Infectious Disease Ontology | curated | `http://purl.obolibrary.org/obo/VIDO_`{.language-plaintext .highlighter-rouge} |
| [vsmo](https://bioregistry.io/vsmo) | Ontology for vector surveillance and management | curated | `http://purl.obolibrary.org/obo/VSMO_`{.language-plaintext .highlighter-rouge} |
| [xl](https://bioregistry.io/xl) | Cross-linker reagents ontology | curated | `http://purl.obolibrary.org/obo/XL_`{.language-plaintext .highlighter-rouge} |

In the *evidence* column, there are a few possible entries:

1. **curated** - this is the URI prefix manually curated in the
 Bioregistry. This happens when the primary ontology artifact uses
 OBO PURLs.
2. **extra** - this is when there's a manually curated extra URI prefix
 in the Bioregistry (in addition to the primary one) that uses an OBO
 PURL. This usually is done to enable the Bioregistry's IRI parser to
 handle cases that appear in third-party data that incorrectly
 constructs IRIs.
3. **biocontext**, **biolink**, and **prefixcommons** - this is when
 other registries have assigned OBO PURLs as their URI expansions

It's worth noting that there are probably *lots* more resources doing
this, e.g., that are listed in
[BioPortal](https://bioportal.bioontology.org/), but have not been
included in the Bioregistry because of their lack of notability,
utility, or reuse.

Here\'s the code that generated the table (before minor modifications)

\`\`\`python import bioregistry from tabulate import tabulate
OBOLIBRARY_SUBSTRING = \"purl.obolibrary.org/obo\" rows = \[\] for
prefix, resource in bioregistry.read_registry().items(): if
resource.get_obofoundry_prefix() or prefix == \"obo\": continue name =
resource.get_name() contact = resource.get_contact() l =
f\"\[{prefix}\](https://bioregistry.io/{prefix})\" if
resource.uri_format and OBOLIBRARY_SUBSTRING in resource.uri_format:
rows.append((l, name, \"curated\", \"\", resource.uri_format)) continue
elif (uri_format := resource.get_uri_format()) and OBOLIBRARY_SUBSTRING
in uri_format: rows.append((l, name, \"default\", \"\", uri_format))
continue for metaprefix in resource.get_mappings(): uri_format =
(getattr(resource, metaprefix, None) or {}).get(\"uri_format\") if
uri_format and OBOLIBRARY_SUBSTRING in uri_format: rows.append((l, name,
\"mapped\", metaprefix, uri_format)) for p in
resource.get_extra_providers(): if OBOLIBRARY_SUBSTRING in p.uri_format:
rows.append((l, name, \"extra\", p.code, p.uri_format))
print(tabulate(rows, headers=\[\"prefix\", \"name\", \"type\", \"code\",
\"uri_format\"\], tablefmt=\"github\")) \`\`\`

## Rationalizations

Based on the table above, there are several situations in which an OBO
PURL appears:

1. Ontologies that are curated in the OBO flat file format then
 converted to the OWL format using
 [ROBOT](https://robot.obolibrary.org/) are automatically given OBO
 PURLs. For example, this occurs for the Livestock Breeding Ontology.
2. Similarly, ontologies that are uploaded to BioPortal likely undergo
 a similar procedure that results in BioPortal PURLs that themselves
 include OBO PURLs. For example, this occurs for FamPlex and the
 Vital Sign Ontology.
3. Ontologies are/were intended to be submitted to the OBO Foundry. For
 example, this includes:
 - The Academic Event Ontology (AEON) is still a work in progress and
 will be submitted to the OBO Foundry
 - The Reagent Ontology (REO) was abandoned and never submitted to
 the OBO Foundry
4. Ontologies that closely used by the OBO Foundry ecosystem, and are
 somtimes mistaken for being in it (e.g., EFO)
5. Not all ontologies, controlled vocabularies, or other semantic
 spaces have associated PURLs. Several registries (e.g., Prefix
 Commons, BioContext, BioLink Model) have "made up" OBO PURLs for
 non-OBO Foundry resources because of their use case-specific
 preferences.
6. In the case of XL, I think that this was an OBO Foundry ontology at
 some point but got renamed. It's very difficult to understand the
 history of the [HUPO Proteomics Standards
 Initiative](http://www.psidev.info/groups/controlled-vocabularies)
 from the outside
7. Some of these examples that appear with evidence "extra" are there
 because third-party resources incorrectly reference entities using
 unsanctioned OBO PURLs
8. In the case of CEMO, it appears the URI prefix is an artifact of
 incorrect configuration curation tooling (likely Protege).

It's hard to know for sure for the situation that lead to the
developers/maintainers of primary resources using unsanctioned OBO PURLs
or the developers/maintainers of third party resources using
unsanctioned OBO PURLs. Regardless, it's still valuable for the
community to know about these problems and potentially use comprehensive
resources like the Bioregistry as a guide towards improving
interoperability and interpretability.