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

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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

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](/2020/12/14/taming-drugbank.html) and
[ChEMBL](/2021/08/05/taming-chembl-sql.html) more actionable. Over the
last year, I've been preparing a concept with the editors of the
[Journal of Cheminformatics](https://jcheminf.biomedcentral.com) on how
to include an assessment of reproducibility to reviews of manuscripts
submitted to the journal. This has resulted in an editorial [Improving
reproducibility and reusability in the Journal of
Cheminformatics](https://doi.org/10.1186/s13321-023-00730-y) as well as
a [call for papers](https://www.biomedcentral.com/collections/irrijc).
In this post, I want to summarize the first generation review criteria
we developed, give an example of it applied in practice

## The Seven (First Generation) Criteria

There are many potential directions for reproducibility. Given the fact
that typical computational scientists are not trained as software
engineers, we decided on seven very simple criteria that can be easily
reviewed and easily addressed:

1.  Does the repository contain a LICENSE file in its root?
2.  Does the repository contain a README file in its root?
3.  Does the repository contain an associated public issue tracker?
4.  Has the repository been externally archived on
    [Zenodo](https://zenodo.org/), [FigShare](https://figshare.com/), or
    equivalent that is referenced in the README?
5.  Does the README contain installation documentation?
6.  Is the code from the repository installable in a straight-forward
    manner?
7.  Does the code conform to an external linter (e.g.,
    [`black`{.language-plaintext
    .highlighter-rouge}](https://github.com/psf/black) for Python)?

These correspond to important details that are complementary to other
considerations of reproducibility, but often overlooked. Throughout the
pilot, the editors and reviewers will try to support authors in
addressing each of these points during revision. I imagine that there
will be future iterations of these criteria as the community begins to
expect these as standard practice. For example, we can narrow criteria 1
to specifically say that the software should be licensed with an
OSI-approved license and not accept science made with non-open licenses.
We could further narrow point 7 to have additional community style
requirements (e.g., passes parts of `flake8`{.language-plaintext
.highlighter-rouge}, as you know I love from my post [on flake8
hell](/2020/04/25/how-to-code-with-me-flake8.html)). We could also
include additional guidelines that e.g. say that the results presented
in the paper should be reproducible with a single command from the
command line, e.g., a shell script. The rabbit hole could go very deep,
so again, it's worth saying that these are very non-controversial
criteria for the first generation.

That being said, many repositories don't follow these! Since these
criteria are so simple, I'm interested in automating their assessment
and further applying it to the entire Journal of Cheminformatics
backlog. I'll describe this more in a future post.

Without further ado, the text below is what I sent verbatim in the
review for [Drug-Protein Interaction Prediction via Multi-View
Variational Autoencoder and Cascade Deep
Forests](https://doi.org/10.21203/rs.3.rs-3242419/v1), which is
pre-printed on Research Square and has associated code
[here](https://github.com/Macau-LYXia/MVAE-DFDTnet). I have tried my
best to include actionable links and information with each piece. I
would like to also automate sending separate GitHub issues for each of
these points as a more concrete to-do list for authors, then also send
an "epic" issue that lists all of them together. With the magic of the
GitHub API, this is possible.

## My First Reproducibility Review for the Reproducibility Pilot

Below, I apply the seven point reproducibility review prescribed by
[Improving reproducibility and reusability in the Journal of
Cheminformatics](https://doi.org/10.1186/s13321-023-00730-y) to the
default branch of repository https://github.com/Macau-LYXia/MVAE-DFDTnet
(commit
[c0858c8](https://github.com/Macau-LYXia/MVAE-DFDTnet/commit/c0858c8cdf61d62f945fbd74d0d60f2531394287)),
accessed on August 27^th^, 2023.

1.  **Does the repository contain a LICENSE file in its root?**  
    No. The GitHub license picker can be used to facilitate adding one
    by following this link:
    https://github.com/Macau-LYXia/MVAE-DFDTnet/community/license/new?branch=main.
    Ideal software licenses for open source software include the MIT
    License, BSD family of licenses, and other licenses approved by the
    [Open Source Initiative](https://opensource.org/licenses). A simple,
    informative guide for picking a license can be found at
    https://choosealicense.com.

2.  Does the repository contain a README file in its root?  
    No. A minimal viable README file contains:

    - A short, one line description of the project
    - Information on how to download, install, and run the code locally
    - Brief documentation describing the single most important use case
      for the repository. For scientific code, this is ideally a
      one-liner in Python code, a shell script, or a command line
      interface (CLI) that can be used to reproduce the results of the
      analysis presented in a corresponding manuscript, use the tool
      presented in the manuscript, etc.
    - Link to an archive on an external system like Zenodo, FigShare, or
      an equivalent.
    - Citation information, e.g., for a pre-print then later for a peer
      reviewed manuscript

    GitHub can be used to create a README file with
    https://github.com/Macau-LYXia/MVAE-DFDTnet/new/main?filename=README.md.
    Repositories typically use the Markdown format, which is explained
    [here](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax).

3.  Does the repository contain an associated public issue tracker?  
    Yes. It is available at
    https://github.com/Macau-LYXia/MVAE-DFDTnet/issues.

4.  Has the repository been externally archived on Zenodo, FigShare, or
    an equivalent that is referenced in the README?  
    No, there is no README. This is also not mentioned in the
    manuscript. See
    https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
    for a tutorial on how to do this.

5.  Does the README contain installation documentation?  
    No, there is no README. This is also not mentioned in the
    manuscript.

6.  Is the code in the repository installable in a straight-forward
    manner?  
    No, the code is not laid out in a typical structure, e.g., as
    described in https://blog.ionelmc.ro/2014/05/25/python-packaging.
    Further, there is no setup configuration that encodes the
    dependencies or facilitates reuse of the code.

7.  Does the code in the repository conform to an external linter (e.g.,
    `black`{.language-plaintext .highlighter-rouge} for Python)?  
    No. The Python code has not been linted, e.g., using
    [`black`{.language-plaintext
    .highlighter-rouge}](https://github.com/psf/black). Similarly, the
    Matlab code has not been linted, e.g. using
    [`checkcode`{.language-plaintext
    .highlighter-rouge}](https://de.mathworks.com/help/matlab/ref/checkcode.html).

Scientific integrity depends on enabling others to understand the
methodology (written as computer code) and reproduce the results
generated from it. This reproducibility review reflects steps towards
this goal that may be new for some researchers, but will ultimately
raise standards across our community and lead to better science. Because
the work presented in this article only yet address one of the seven
points of the reproducibility review, I recommend rejecting the article
and inviting later resubmission following addressing the points.

For posterity, this review has also been included on
https://github.com/Macau-LYXia/MVAE-DFDTnet/issues/1.

## The Future is Looking Good

The example above isn't so great - it's possible that these authors have
never considered most of these points about reproducibility before. The
reality is that many computational scientists are not trained in this
since their mentors were not primarily trained as computational
scientists themselves. Combine with the perverse incentive structure in
academia, it's understandable how this can be left out from some
publications. I experienced something similar in my doctoral studies,
and had to bootstrap my own philosophy on reproducibility as well as the
practical skills to achieve it. I also understand not everyone is in the
position where they have the flexibility/freedom/initiative to do this.

That all being said, we are now entering an era where progressive and
newly minted PIs actually have training as computational scientists. The
next paper in my queue for a reproducibility review is for
https://github.com/Steinbeck-Lab/cheminformatics-python-microservice,
which will pass the 7 criteria with flying colors. I'm looking forward
to the future when we expect more excellent science on the regular. See
you there!

------------------------------------------------------------------------

I'm not sure how people will view the way I talk about reviews - I am
quite open with posting reviews on GitHub and also openly discussing the
fact that I've reviewed something. Ideally, I don't accept reviews for
papers that don't have pre-prints, since I personally think the review
process should be open. I hope it's the case that I haven't been rude or
unfair. If that's the case, someone can help me change the way I write
about these topics.
