Maria Levchenko

# **Europe PMC POSI update -- 2 years on ** {#europe-pmc-posi-update-2-years-on .wp-block-heading .has-medium-font-size}

Two years have sailed by since Europe PMC adopted the Principles of Open
Scholarly Infrastructure (POSI) in February 2021. POSI is a set of
guidelines for open scholarly infrastructure providers and outlines how
these organisations should be run and sustained. It offers a framework
to uphold transparency and accountability. Since Europe PMC joined the
POSI adopter group, the [POSI
Posse](https://openscholarlyinfrastructure.org/posse/), it has grown to
15 organisations. In this time the POSI principles have progressed to
[Version 1.1](https://openscholarlyinfrastructure.org/), as a result of
work in which Europe PMC was involved.

The POSI principles enable organisations to measure progress on the 16
principles using a traffic light system. In our [original blog
post](https://blog.europepmc.org/2022/02/europe-pmc-adopts-the-principles-of-open-scholarly-infrastructure.html),
we completed this exercise and indicated our level for all of the
principles, as shown below.

**Governance**

🟢  Coverage across the research enterprise

🟢  Stakeholder governed

🟢  Non-discriminatory membership

🟢  Transparent operations

🟢  Cannot lobby

🟡  Living will

🟢  Formal incentives to fulfil mission & wind-down

**Sustainability**

🟡  Time-limited funds are used only for time-limited activities

🔴  Goal to generate surplus

🔴  Goal to create contingency fund to support operations for 12 months

🟢  Mission-consistent revenue generation

🟢  Revenue based on services, not data

**Insurance**

🟡  Open source

🟢  Open data (within constraints of privacy laws)

🟢  Available data (within constraints of privacy laws)

🟡  Patent non-assertion

No traffic lights have changed colour, but in this post we indicate
where we have made significant progress.

Open source software is one of the POSI insurance components, along with
open and available data and patent non-assertion. POSI states that all
software and assets required to run the infrastructure should be
available under an open-source licence. 

Europe PMC has focussed on the open source principle in the past two
years and has made significant progress as part of Europe PMC's
continuous open source transition. All of Europe PMC's open source
software is available via our
[public-projects](https://gitlab.ebi.ac.uk/literature-services/public-projects)
GitLab repository, which now contains 27 open projects. Since the last
POSI review, we continue to apply the open source principle to any new
code bases we develop. Where possible we also update and make our legacy
systems publicly available, cementing our commitment to open source.

One of the fundamental advantages of open source is community
involvement. Below we highlight how our open source journey has
increased Europe PMC's impact and supported innovation and discovery as
part of our mission. 

# Open source projects for text-mining applications {#open-source-projects-for-text-mining-applications .wp-block-heading .has-medium-font-size}

Europe PMC uses dictionary-based
[text-mining](https://blog.europepmc.org/2023/03/introducing-europe-pmc-annotated-full-text-corpus-for-bioentities-and-associations.html)
to find biological entities, for example, gene names or organisms,
citations to biological databases, and accession numbers mentioned in
journal publications and preprints. Recently we have developed a new
tool -- a text-mining API -- that extends this process to new types of
content. This tool is now employed in Europe PMC to identify concepts of
interest in supplementary files to unlock additional evidence associated
with the article.

To enable reuse we have made the code and dictionaries required to run
our text-mining infrastructure openly available. This permits other
organisations to analyse data sources not currently available in Europe
PMC. BioModels, an EMBL-EBI database for mathematical models of
biological systems, plans to repurpose this software to enrich existing
data by annotating biological models with gene ontology terms. In
another example, the German Collection of Microorganisms and Cell
Cultures at Leibniz Institute DSMZ is investigating how this tool can be
used to extract details about relevant microorganisms from biological
patents.

As a result of a collaboration with Open Targets, machine learning was
applied to extract evidence from scientific literature for drug target
identification and validation. This combined Named Entity Recognition
(NER) for identifying genes/proteins, diseases, organisms, and
chemicals/drugs within scientific texts, and entity normalisation to
accurately map these entities to databases like Ensembl, Experimental
Factor Ontology (EFO), and ChEMBL. The results are accessible through
Europe PMC's text-mining infrastructure. We are currently developing and
extending the models to replace our dictionary-based text-mining
applications. This work is being executed in the open via the Europe PMC
[GitLab](https://gitlab.ebi.ac.uk/literature-services/public-projects)
site.

A previous project by Dr. Maaly Nassar developed a [machine learning
framework to enrich metagenomics
data](https://blog.europepmc.org/2020/11/enriching-europe-pmc-publications-with-metagenomics-annotations.html)
in MGnify, the microbiome sequence data analysis resource. As an
outcome, Europe PMC's collection of open access publications was
annotated with metagenomic terms. Extending this effort to new articles
as they become available in Europe PMC required further work. For
example, compressing machine learning models to ensure sustainability
and reduced computation. The new metagenomics pipeline and underlying
machine learning models are being developed as open source in
collaboration with SureChembl and PBDe. SureChembl will use the machine
learning architecture and dictionaries to mine patents for biological
entities including chemical/drugs, gene-proteins, diseases and organisms
and PDBe will use it to mine important residues in proteins from
scientific articles, further delivering value to Europe PMC. This
collaboration will advance the utility of the Europe PMC annotations
platform, through improved annotation and discovery tools. This has
enabled dual benefits and reduced direct workloads for all teams.

# Open source projects for new publication models {#open-source-projects-for-new-publication-models .wp-block-heading .has-medium-font-size}

Supporting open science and emerging open publication workflows is a
strategic goal for Europe PMC. Recognising the importance of preprints
in the life sciences, we have taken steps to build trust, improve
discoverability, and support preprint reuse.

Europe PMC incorporates preprints from over 30 preprint servers.
Preprint information is pulled into Europe PMC from Crossref -- a DOI
registration agency used by many preprint providers. Europe PMC uses the
Crossref REST API to retrieve preprint abstracts and metadata. The
legacy software used to fetch and store this data in an Oracle database
has been converted to open source. This code can now be reused by other
tools and services that aggregate preprints across different platforms.

To support preprint evaluation Europe PMC [links preprints with
associated
reviews](https://blog.europepmc.org/2024/01/discovering-reviewed-preprints.html).
This is accomplished in collaboration with Sciety and EMBO's Early
Evidence Base -- two services that collate preprint reviews from
different initiatives. Both Sciety and Early Evidence Base share review
information in the DocMaps format. To enable DocMaps adoption by the
preprint review community we have developed a DocMap parser. This tool
converts DocMap files into JATS XML, a format widely used by the
scholarly communications community. The parser code is open and
available for reuse and we hope this will support further growth around
the use of the DocMaps framework.

# Next chapter {#next-chapter .wp-block-heading .has-medium-font-size}

Europe PMC is committed to providing open data supported by high
quality, sustainable, open and community driven infrastructure. This
re-audit demonstrates the efforts Europe PMC has achieved since our
commitment to the principles in 2021 to increase our open source code
proportion.

As a grant funded resource set within the context of EMBL, Europe PMC
cannot create a *goal to generate surplus* or a *goal to create
contingency funds* to support operations for 12 months. Europe PMC is
one of the open biological [data
resources](https://www.ebi.ac.uk/services) managed by EMBL-EBI. In
February 2024 EMBL published a [long-term data
preservation](https://www.ebi.ac.uk/long-term-data-preservation)
statement. This statement provides greater transparency regarding
sustainability plans for EMBL-EBI data resources and highlights grounds
for Europe PMC's resilience despite the lack of an individual *living
will* or *commitment to time-limited funds being used only for
time-limited* *activities* because it exists within the context of many
other databases run by EMBL-EBI, which already has a history of
responsible data resource life cycle management and retirement. EMBL
does not have a *Patent non-assertion covenant* but the [Open Science
and Open Access
Policy](https://www.embl.org/documents/document/internal-policy-no-71-open-science-and-open-access/)
asserts "EMBL expects (...) software to be Open Source by default in
both services and research, and made available in open/community
software repositories".

Since adopting the POSI principles, Europe PMC was selected by the
Global Biodata Coalition as a [GBC Global Core Biodata
Resource](https://globalbiodata.org/what-we-do/global-core-biodata-resources/)
in December 2022; further indicating Europe PMC is of fundamental
importance to the wider life-science community and the long-term
preservation of biological data. Europe PMC is at the heart of open
science. It provides comprehensive access to life sciences literature
and is available to anyone, anywhere for free. As such, ensuring its
sustainability as a critical resource is vital.


**Europe PMC POSI update – 2 years on **   Two years have sailed by since Europe PMC adopted the Principles of Open Scholarly Infrastructure (POSI) in February 2021. POSI is a set of guidelines for open scholarly infrastructure providers and outlines how these organisations should be run and sustained. It offers a framework to uphold transparency and accountability.

Messaggi di Rogue Scholar

Moving to open source