Charles Tapley Hoyt

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.


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.

Messaggi di Rogue Scholar

Resources masquerading as OBO Foundry ontologies