Blog - Europe PMC

Improved affiliation search for grants

2023-03-28T10:36:00.000+01:00

Integrating ROR IDs in Grant Finder

Funding and research organisations are increasingly looking to understand the impact of the research they support. To link institutions with grant awards from Europe PMC funders the Europe PMC Grant Finder tool now incorporates Research Organization Registry (ROR) IDs.

Linking grants and institutions

The Grant Finder tool from Europe PMC allows users to search and access information about 98,000 biomedical research grants from 37 Europe PMC funders. This information includes the affiliation of the principal investigator, who is awarded the grant. However, a search for grants by institutional affiliation can miss relevant entries due to variations in institutional names.

For example, the same organisation may be referred to as University of Cambridge, Cambridge University, etc.

Screenshot of the Grant Finder prior to the ROR ID integration. Affiliation drop-down menu suggests multiple options for the same organisation.

A ROR ID is an open persistent identifier for research organisations. It helps disambiguate names for over 102,000 institutions. ROR makes it easy for anyone to connect research organisations to research outputs.

To improve the affiliation search function of the Grant Finder tool we have decided to map institutions in the Europe PMC grant database to corresponding ROR IDs.

Integrating ROR IDs

At the start of this project some Europe PMC funders were already providing ROR IDs in the funding data they supplied. However as of July 2022 only ~10% of grants in Europe PMC were linked to a ROR ID.

To assign ROR IDs to remaining affiliations, we have used an automated script to query the ROR REST API for the ~23,000 institution names in the grants database. The ROR API response includes not only a matching ROR ID, but also the matching confidence score and the type of matching algorithm applied. Importantly, it provides a binary indicator of whether the score is high enough to consider the organisation correctly matched.

Using the ROR API we were able to confidently match 41% of institutions. This was followed by a manual check for any potential errors. Institutions associated with multiple grants were prioritised in this step.

As a result, over 80% of grants in Europe PMC now have a ROR ID associated with the principal investigator’s institution. Over 2600 unique ROR IDs are recorded in the Europe PMC grants database and can be retrieved programmatically as part of the GRIST API core response.

Screenshot of the GRIST API core response query for (gid:081052) with institution name and ROR ID highlighted in red.

Improved grants search

To streamline user experience we then used the ROR ID to suggest matching affiliations in the Grant Finder search. When users enter an affiliation into the Grant Finder search, the auto-suggestion feature will display a single name for institutions associated with a ROR ID, consolidating different institutional aliases. The feature also displays the ROR ID in brackets.

Screenshot of the Grant Finder after the ROR ID integration. Affiliation drop down menu consolidates aliases for Cambridge University under the organisation’s primary name - ‘University of Cambridge’, with the ROR ID displayed in brackets.

Future plans

Our ambition is to enable grant search by ROR ID of the associated institution. In the current implementation, only the institution name is used for affiliation search via the GRIST API and the Grant Finder tool.

The current integration primarily supports research funders, who want to view grant allocations through an institutional lens. However, we believe that it creates many opportunities for wider adoption. Lessons learnt from incorporation of ROR IDs into the grant data could help with future steps, for example, enriching publications with ROR IDs.

Supporting innovation by integrating related research outputs is an important part of Europe PMC’s mission. Over the years we have built a rich network of research objects connected via persistent identifiers. This includes DOIs/PMIDs/PMCIDs for journal articles, PPRIDs for preprints, ORCIDs for research authors, accession numbers and DOIs for data, and Grant IDs and DOIs for grants. We hope that addition of ROR IDs to Europe PMC will pave the way for new tools that build on this interconnected network of research.

Introducing Europe PMC Annotated Full-text Corpus for bioentities and associations

2023-03-08T12:02:00.003+00:00

Europe PubMed Central (Europe PMC) is an open access repository of life science research, including peer-reviewed journal articles and preprints. It contains over 41 million abstracts and 8.7 million full-text articles, adding over 1.7 million new articles annually. To facilitate information discovery and foster literature–data integration, Europe PMC has incorporated text-mining approaches into its workflows.

Text-mining is a powerful tool used in the field of biomedicine to extract relevant information from large amounts of text data, such as research papers, clinical reports, and patient records. It involves using machine learning algorithms and natural language processing techniques to identify key concepts and relationships between words and phrases in the text.

With millions of new research papers published every year, it's impossible for researchers to read and synthesise all of the information available manually. Text-mining algorithms can be used to automatically extract key concepts, relationships, and findings from scientific papers, allowing researchers to quickly identify relevant information and stay up-to-date on the latest developments in their field.

At Europe PMC, the SciLite Annotations tool uses text-mining to highlight terms in research articles and preprints, allowing users to quickly scan the article for relevant concepts, such as diseases, chemicals, or protein interactions. Europe PMC contains ∼1.3 billion annotations sourced in-house and from 10 external providers. The annotations platform covers multiple annotations types including bioentities ranging from accession numbers to Open Targets gene–disease relationships. Users can programmatically access the annotations using the Annotations API, reducing the time requirement of extracting facts and evidence to help advance the discovery process.

How Europe PMC developed annotations for named entities

Europe PMC has developed annotations for Gene/Protein, Disease, Organism and Chemical bioentities. For this purpose, established ontologies are being used as dictionaries to pattern match the entity-terms from the text. For example, the Unified Medical Language System (UMLS) ontology is used for tagging diseases mentioned in articles. Although the dictionary-based approach is easy to understand and to implement, an exhaustive list of patterns are required to recall more entities and require regular updating to remain current. Moreover, with the contextual information missing, this creates ambiguity, especially with the use of acronyms and abbreviations by scientists writing papers. For example,Cockayne syndrome Group A and Corporate Social Responsibility are both abbreviated to CSA. Overall, this approach has multiple challenges, which cause false positives, false negatives, and other technical issues, as listed below:

False positives

Short target names are confused with ambiguous abbreviations.

Cockayne syndrome Group A (CSA) vs Corporate Social Responsibility (CSA)

Contextual differences to identify terms

Hearing (aids) vs AIDS the disease

Common English words

CAN gene vs ‘can’ being a common English word

Multiple entities or mentions of compound entity

It is difficult to pattern match BRCA1 and 2 or BRCA1/2 vs BRCA1 and BRCA2

False negatives

Missing of entities that do not exist in the original ontology/dictionaries

E.g., T2D for Type 2 Diabetes Mellitus
The ontology shall be updated regularly to keep up with the growing literature

Technical issues

Encoding issues often create garbage values when converted from ascii to UTF-8 format

TNFα vs TNFα

Sentence boundary problems

It is difficult to delineate a sentence within a caption of a Figure or a Table

Challenges faced when using a dictionary-based approach to annotate entities in scientific text including false positives, ambiguity of abbreviations, special characters, and a lack of distinction between genes and proteins.

Improving annotations using machine learning: gold standard dataset

To address the challenges of using a dictionary-based approach to annotations the Data Science team at Europe PMC has explored the use of machine/deep learning techniques.

To train any machine-learning algorithm, a gold standard dataset of annotations is needed. While corpora without annotations are good for learning semantics, text-mining tools trained on human-annotated corpora outperform those trained on non-annotated ones. Therefore, open-source gold-standard datasets are crucial for improving biomedical text-mining systems. Based on this information, the team methodologically developed an annotated full-text corpus based on annotation guidelines. The corpus is a collection of 300 research articles from the Europe PMC open access subset. The selected articles have been annotated by humans to indicate mentions of three biomedical concepts: Gene/Protein, Disease, and Organism. The annotation guidelines were used by the human annotators to select the correct text span and type of annotation.

Problems faced while developing the gold standard dataset

The Europe PMC team faced several challenges in creating a gold standard training set to support machine learning approaches for entity extraction. One of the first hurdles was to select a small number of representative articles from the several million available in the Europe PMC database. For this purpose a strategy was designed and several techniques were employed to stratify articles and select the representative set.

Out of approximately 6 million full-text articles in the Europe PMC repository, archived on the 31st of August, 2018 (v2018.09), approximately 1 million were open access with a creative commons licence and could be included in the training set. The training set was further refined by the following criteria: article sizes between 25 and 50 KB were selected, which resulted in a collection of approximately 0.5 million articles. This was followed by sorting the articles with the entity mentions into low, medium, and high ‘bins’ for each entity type, that is Gene/Protein, Disease, and Organisms. Articles containing small or no mentions of any of the entities were discarded, leaving over 460,000 articles of which 300 were randomly selected. The final stage of the strategic workflow included working with the annotators iteratively to improve the annotation guidelines.

Collaborating with Molecular Connections to annotate the corpus

Europe PMC collaborated with Molecular Connections to annotate the corpus. The annotators were asked to use the hypothes.is tool, which was added onto Europe PMC as a plug-in to support collaborative efforts for the annotation work. Annotators saved their annotations to the hypothes.is server in JSON format, which was retrieved and converted to CSV format using in-house tools. This project used a triple-anonymous approach to annotation; three annotators annotated the same articles independently to ensure annotation quality and validate inter-annotation agreement. Annotation discrepancies were resolved by the majority vote to achieve/ensure the best quality annotation. That is, at least two annotators must agree on the annotation boundary and the entity type of the entity terms to pass the acceptance threshold. This maximised the total number of annotations. For example, if one annotator misses a term, it will likely be picked by the two other annotators. The triple-anonymous method made it possible to conveniently assess the inter-annotator agreements to ensure the annotation quality. Using this approach, we were able to increase the annotations’ accuracy from 70% to 99%.

What can you do with the Europe PMC open source corpus?

The Europe PMC Annotations Corpus is among the largest human-annotated biomedical corpora publicly available. The corpus also comes with scripts that were used to clean and format the annotations from the Hypothes.is platform. The dataset is also available in the IOB format for input to deep learning algorithms. In addition, the annotation guidelines are also made available for researchers to improve/compare conclusions drawn from the results.

This open source gold-standard dataset can be used to improve the accuracy and reliability of life science natural language processing tools such as entity recognition, supporting advancements in scientific research. Furthermore, the corpus can support clinical decision-making by providing access to relevant clinical information that can be used to develop clinical decision support systems, which could improve patient outcomes and reduce healthcare costs.

The Annotated Corpus can accelerate life science research by providing large amounts of accurately labelled data that can be used to train machine learning models for various applications, including drug discovery and disease diagnosis. For example, the deep learning models that were trained using the Europe PMC Annotations Corpus are now being used for literature mining for Open Targets to identify and prioritise drug targets, provide evidence for drug target validation, and support drug repurposing efforts to accelerate and improve the efficiency of drug development.

To find out more about the Europe PMC Annotations Corpus and details on how to access and reuse this open community resource:

View webinar recording: https://bit.ly/MLWebinarReg
Read the preprint: Europe PMC Annotated Full-text Corpus for Gene/Proteins, Diseases and Organisms

Written by Santosh Tirunagari, Senior Machine Learning Developer at EMBL-EBI

Europe PMC in 2022: a year in review

2023-01-11T11:15:00.000+00:00

With the start of the new year Europe PMC reflects back on the year 2022. As many of us adjusted to hybrid working, with the opportunity to return back to the office, meet new colleagues, and attend conferences and workshops in person again for the first time since the pandemic, Europe PMC’s efforts continued to concentrated on open access to research, building trust in preprints, user-centred design, and long term sustainability.

Preprint highlights

In 2022, in line with our open access commitment, Europe PMC has increased the number of preprints available with the inclusion of five new preprint platforms: SciELO Preprints, Access Microbiology, ARPHA preprints, agriRxiv, and EcoEvoRxiv. Over 520,000 preprints from 28 preprint servers are now freely discoverable in Europe PMC.

Following the success of full text COVID-19 preprints in Europe PMC, conversion of full text preprints funded by Europe PMC funders was launched in April 2022, to improve the discoverability of science reported in preprints, and increase the visibility of research supported by Europe PMC funders. These full text preprints are available via the Europe PMC website, as well as automated bulk download for text-mining and programmatic analysis.

For those interested in reviewing preprints in a journal club setting Europe PMC ran a webinar on how to use Europe PMC to select and evaluate preprints. Europe PMC also expanded the number of preprint review providers in Europe PMC by the inclusion of public preprint evaluations available from Sciety, a preprint review platform.

Finally, to help increase transparency and build trust in preprints, Europe PMC developed the Article status monitor tool, which can alert researchers when a preprint is withdrawn or removed, published in a journal, or has a new version. For further information and to learn more about the tool, see this poster presented by Europe PMC at the Reproducibility, Replicability and Trust in Science conference.

Service for users

Europe PMC places users at the heart of innovation. To provide even more powerful and customisable search tools, user research was carried out to inform the redesign of the advanced search and main search functionality. Based on what was learnt, some changes have already been implemented – for example, changing the default sort order to relevance. Europe PMC also completed a user research study investigating ways to collate and display preprint peer review status to help build trust in preprints. Preprint review is an area of increasing interest to the research community, and therefore an important part of the Europe PMC roadmap. For more information on Europe PMC’s user research and future plans in this area see our lightning talk at the Recognising preprint peer review conference.

A site-wide user survey was launched in November, to better understand how you use Europe PMC, what you like about it, and where improvements can be made. The survey results will help guide the development of many exciting projects that we can’t wait to share with you! Keep up to date with us by following @EuropePMC_news on Twitter. Europe PMC is always keen to learn from user feedback and hopes that a new and improved design of the feedback form will make sharing your thoughts easier than ever.

Sustainability

There are a number of ways work on the long term sustainability of Europe PMC has been approached this past year.

In February 2022 Europe PMC adopted the Principles of Open Scholarly Infrastructure (POSI) – a set of guidelines by which open scholarly infrastructures can be operated and sustained. The Europe PMC review against POSI demonstrated our commitment to provide high quality, sustainable, open, and community driven infrastructure, and highlighted potential improvements to increase the proportion of open source code Europe PMC is run on.

In December, Europe PMC was announced as a Global Core BioData Resource by the Global BioData Coalition, demonstrating the need for the long term funding and sustainability of Europe PMC as a critical global life science and biomedical research infrastructure.

To this end, Europe PMC was excited to announce that it has welcomed three new funders to the Europe PMC funder family in 2022. The Medical Research Foundation funds research that will ‘advance medical research, improve human health and change peoples lives’. Health and Care Research Wales focuses on health and social care, with their goal ‘to ensure that today’s research makes a difference to tomorrow’s care’. The European and Developing Countries Clinical Trials Partnership (EDCTP) funds clinical research in line with their vision ‘to reduce the individual, social and economic burden of poverty-related infectious diseases in sub-Saharan Africa’. All Europe PMC funders expect research they fund to be made openly available, and we delivered a webinar explaining how to make research open with Europe PMC.

To help address the urgent challenges of climate change seen across the globe, and in line with EMBL’s sustainability strategy, Europe PMC has worked hard to migrate services to a new high performance computing farm to reduce our energy consumption and resultant impact on the planet.

Final remarks

Europe PMC is dedicated to providing an exceptional free and open service for the scientific community that meets your needs. Europe PMC will continue to be guided by user feedback as part of its mission to support innovation and discovery by engaging users, enabling contributors, and integrating related research outputs.

Take a look at the plans for 2023 on Europe PMC’s Roadmap and let us know what you think!

Medical Research Foundation joins Europe PMC

2022-06-20T10:03:00.003+01:00

We are delighted to announce that the Medical Research Foundation joins Europe PMC as a new funder. This brings the Europe PMC funder family to 37 members.

The Medical Research Foundation is the charitable foundation of the Medical Research Council. With support from the scientific and medical communities and the public, the charity funds high-quality medical research that improves human health and changes people’s lives. The Foundation is a purely research-led organisation, meaning all its efforts are centred around funding scientists and research. This allows them to focus solely on finding and funding research that has the potential to change lives now, or may become important in the future.

Researchers funded by the Medical Research Foundation will join thousands of others who make their published research articles freely available from Europe PMC as soon as possible without any embargo period. If your research is supported by the Medical Research Foundation you can submit your published manuscript for inclusion in Europe PMC via Europe PMC plus manuscript submission system.

You can now find publications supported by the Medical Research Foundation, as well as Medical Research Foundation grant awards via Europe PMC search and the Grant finder tool.

For more information about joining Europe PMC funder group, visit our website: http://europepmc.org/Joining

Health and Care Research Wales joins Europe PMC funders group

2022-05-17T16:58:00.002+01:00

We are delighted to announce that the Health and Care Research Wales joins Europe PMC as a new funder. This brings the Europe PMC funder family to 36 members.

Health and Care Research Wales is a networked organisation which brings together a wide range of partners across the NHS in Wales, local authorities, universities, research institutions, third sector, and others. Health and Care Research Wales aims to ensure that today’s research makes a difference to tomorrow's care. To achieve this goal Health and Care Research Wales brings together partners to promote research into diseases, treatments, and services, which can lead to discoveries and innovations to improve and save lives. Health and Care Research Wales is supported by the Welsh government.

Health and Care Research Wales researchers will join thousands of others who have made a commitment to making research open access through inclusion of research articles in Europe PMC. Health and Care Research Wales requires all peer-reviewed research articles submitted on or after 1st September 2022 to be published under the Creative Commons attribution licence (CC BY) (or Open Government Licence (OGL) when subject to Crown Copyright), made open access, and to be included in Europe PMC as soon as they are published without any embargo period. Authors are strongly encouraged by Health and Care Research Wales to self-archive peer-reviewed research articles submitted before 1st September 2022 in Europe PMC. If your research is funded by Health and Care Research Wales you can submit your published manuscript for inclusion in Europe PMC via Europe PMC plus manuscript submission system.

Europe PMC improves discoverability of preprints

2022-05-03T12:08:00.001+01:00

Europe PMC now includes the full text preprints supported by Europe PMC funders

Open science is at the heart of Europe PMC, providing access to open content and data. Recognising the role that preprints play as a way for life science researchers to openly and rapidly share their findings, Europe PMC has made over 420,000 preprint abstracts from 24 preprint servers discoverable alongside journal publications. Following the success of the COVID-19 full text preprints initiative, which currently includes over 31,000 full text COVID-19 preprints, Europe PMC is expanding the number of searchable full text preprints to include those supported by Europe PMC funders. Overall this new project aims to increase the discoverability of science reported in preprints, expand the collection of full text preprints for future analyses, as well as improve visibility of preprints supported by Europe PMC funders.

Which preprints are included?

From April 1st 2022, Europe PMC includes the full text of preprints that acknowledge funding from at least one of the 36 Europe PMC funders and have a Creative Commons licence. As the first step Europe PMC has added preprints from medRxiv, bioRxiv, and Research Square, with plans to expand to other preprint servers in the future.

How does it work?

Europe PMC converts the freely available full text in PDF format to a machine-readable XML format suitable for text-mining. A preview of how the preprint will appear in Europe PMC is then shared with the corresponding author. The full text is added to Europe PMC two weeks later or immediately after author approval. The full text of preprints supported by Europe PMC funders is made searchable along with other preprint abstracts through the Europe PMC website as well as programmatically via the API. It is also available for bulk download as part of the Preprints subset for future analyses.

What are the benefits?

While the full text of each preprint is openly available from the corresponding preprint server, there are numerous advantages to including it in Europe PMC.

Being able to view the full text directly on Europe PMC makes it more convenient to users and makes research presented in preprints more discoverable. For preprint authors supported by Europe PMC funders this means higher visibility and wider reach for their scientific findings.

By default Europe PMC search applies to the full text of journal articles and preprints that are indexed, not just abstracts. Therefore, having the full text of these preprints within Europe PMC means that they are surfaced if terms searched for are beyond their abstract. It also enables advanced search options, for example the ability to limit search to specific sections of the preprint, for example Figures, Results, or Methods.

Making the full text of preprints available programmatically in a structured machine-readable format also supports text and data mining. The Europe PMC text and data mining pipeline, in collaboration with several text-mining groups, identifies key biological entities, such as data accessions or gene/protein names, experimental methods, protein interactions, mutations, gene-disease relationships and more, in the abstracts and available full text of preprints. This enables better linking of the literature and the data behind it. The text mining pipeline powers the Annotations tool, which allows readers to quickly scan preprints of interest to find data and evidence presented in the manuscript.

Full text can also support future research on research, for example around the impact of peer review or data availability. For users carrying out bioinformatic studies or literature reviews, having open access to the full text preprint collection from multiple preprint servers both on the website and programmatically via RESTful APIs in Europe PMC makes analysis easier and further supports open sharing of data.

Finally, as an archive of scholarly content, Europe PMC contributes to longevity and continued access to scientific data and findings presented in preprints. We believe that preprints can remove barriers to open science and Europe PMC is committed to making the science reported in preprints more widely discoverable.

For more information about preprints in Europe PMC, visit our website: https://europepmc.org/Preprints

SciELO Preprints discoverable in Europe PMC

2022-03-03T09:11:00.000+00:00

We are delighted to announce that SciELO Preprints are now discoverable in Europe PMC.

SciELO (Scientific Electronic Library Online) is a bibliographic database, digital library, and cooperative electronic publishing model of open access journals. It was originally established in Brazil in 1997 and has since expanded to include collections from 16 countries, predominantly in Latin America.

In 2020 SciELO and the Public Knowledge Project (PKP) launched the SciELO Preprints Collection to accelerate the availability of research articles and other scientific communications.

As an avid supporter of open science, Europe PMC has been indexing life science preprints alongside journal articles since 2018. Currently, over 400,000 preprints from over 20 different platforms are available in Europe PMC. Preprints in Europe PMC are enriched with links to open peer review materials, related data, citing articles, and other useful resources.

Over 1000 SciELO Preprints are available in Europe PMC in their original language, Portuguese, Spanish, or English, and can be accessed using the following search: PUBLISHER:"SciELO Preprints".

An example of a SciELO preprint in Europe PMC.

The preprint page displays the title, abstract, and author information. The preprint is linked to the journal published version from the preprint banner, as well as preprint reviews, including the recent integration between SciELO Preprints and PREreview, and also to the citation information and alternative metrics from the Citations & impact section on the left hand side. Readers can view genes, diseases and organisms mentioned in the preprint under the Annotations tool on the right hand side. The preprint can also be easily added to the ORCID profile by the authors using the Claim to ORCID option on the right.

An important outcome of the new collaboration between Europe PMC and SciELO is the push for changes to scholarly infrastructure to better handle multilingual content. Support for multilingual metadata is now part of Crossref’s public roadmap. Implementation of these changes would enable Europe PMC to host Portuguese, Spanish, and English versions for SciELO Preprints. But much more importantly, it could mean greater accessibility and discoverability of multilingual research across many scholarly platforms.

If you are interested to learn more about SciELO Preprints in Europe PMC, please register to join our live demo at 14.00 (GMT) on April 13th.

Europe PMC adopts the Principles of Open Scholarly Infrastructure

2022-02-21T09:44:00.000+00:00

As a long-standing service and infrastructure provider in the open science ecosystem, Europe PMC supports the Principles of Open Scholarly Infrastructure (POSI). We welcome the momentum gathering behind this initiative to promote the need to support and sustain the open infrastructure.

Europe PMC has been a part of the public and open infrastructure for over 15 years and is run and managed by EMBL-EBI (which is part of the pan-European organisation of EMBL). It is funded by 34 international funders and is community-driven, open infrastructure, set in the context of key global open data resources such as the European Nucleotide Archive (INSDC), the wwPDB and the European Genome-Phenome Archive. All of these resources exist for the public good, led by scientific need and international collaborations, and have open governance structures and a commitment to long-term sustainability. Together with PMC USA, Europe PMC is a part of the PubMed Central International archive network, which plays an integral part in fulfilling shared goals to enable international open science. Europe PMC has been selected as an ELIXIR Core Data Resource, which means that it is of fundamental importance to the wider life-science community and the long-term preservation of biological data.

Since the original POSI blog post by Bilder, Lin and Neylon (2015), a number of organisations that provide open infrastructure have adopted the principles, for example Crossref, ROR, OurResearch and DataCite, many of which Europe PMC collaborates with.

We decided to test the Europe PMC open infrastructure against POSI. By completing the review we were able to identify areas of the principles that align, but also others that do not map well to publicly funded services and organisations. We hope that the details below will provide another use case to extend POSI to include a greater diversity of open infrastructures.

We also thank Geoffrey Bilder (one of the authors of POSI) and Ed Pentz from Crossref for a constructive discussion about POSI and their perception of the principles and how Europe PMC aligns with them.

How Europe PMC meets the Principles of Open Scholarly Infrastructure (POSI)

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

Governance

🟢 Coverage across the research enterprise

It is increasingly clear that research transcends disciplines, geography, institutions and stakeholders. The infrastructure that supports it needs to do the same.

Europe PMC focuses on content and data from the life sciences, however Europe PMC contains content that is cross-disciplinary, for example from social sciences, chemistry and physics. The infrastructure and content ingest process in both cases is generic and utilises cross-discipline community standards (such as the JATS XML data model used by the publishing community to structure scholarly content). Therefore, the infrastructure is discipline agnostic. Content comes from worldwide sources and the users are worldwide.

🟢 Stakeholder governed

A board-governed organisation drawn from the stakeholder community builds more confidence that the organisation will take decisions driven by community consensus and consideration of different interests.

Europe PMC’s governance includes a Scientific Advisory Board and Funder Committee. The Scientific Advisory Board includes representative members of the open science community, including researchers, publishers, funders and text miners.

Europe PMC’s Funder Committee includes representatives of the 34 international funders who support Europe PMC. Current members of these groups can be found on the Europe PMC Governance page.

🟢 Non-discriminatory membership

We see the best option as an “opt-in” approach with a principle of non-discrimination where any stakeholder group may express an interest and should be welcome. The process of representation in day to day governance must also be inclusive with governance that reflects the demographics of the membership.

We have assumed for the purposes of this principle that ‘members’ of Europe PMC are funders and we operate a principle of non-discrimination and any members are welcome. There are two criteria to join Europe PMC as a funder. Funders must be:

Public organisations whose legal mission is research funding, or;
not-for-profit organisations (charities, foundations, associations) that fund research as a part of their mission.

Europe PMC also provides various services that anyone in the community can engage with, such as external links, preprints ingest and the annotations submission service. Use of these services is non-discriminatory but there are required criteria for participation. For example, preprints must meet certain minimum metadata standards and external links should be open and free to access and add value to the content.

🟢 Transparent operations

Achieving trust in the selection of representatives to governance groups will be best achieved through transparent processes and operations in general (within the constraints of privacy laws).

The Europe PMC Funder Committee terms of reference define the process and criteria for new funders joining.

Europe PMC receives external grant funding and in-kind support from EMBL. Details of Europe PMC funding, which is provided by 34 funders of life science research and coordinated by Wellcome Trust, are available via Europe PMC’s grant finder. Details of how EMBL-EBI is funded are provided in the annual report.

Europe PMC undertakes user research and outreach activities on an ongoing basis to identify community and user needs. These are translated into new features and improvements, as appropriate. Europe PMC publishes a quarterly roadmap and in addition has published anonymised user research findings on Figshare.

🟢 Cannot lobby

The community, not infrastructure organisations, should collectively drive regulatory change. An infrastructure organisation’s role is to provide a base for others to work on and should depend on its community to support the creation of a legislative environment that affects it.

Europe PMC responds to regulatory changes, but does not lobby for them, or drive them. Europe PMC supports changes to funders’ open access policies. We contribute to the development of community standards, for example preprint metadata standards. Europe PMC responds to the needs of its community, for example by ingesting COVID-19 preprints and grants.

🟡 Living will

A powerful way to create trust is to publicly describe a plan addressing the condition under which an organisation would be wound down, how this would happen, and how any ongoing assets could be archived and preserved when passed to a successor organisation. Any such organisation would need to honour this same set of principles.

EMBL is an intergovernmental organisation, powering world-class research through tools, data and facilities. EMBL was established nearly 50 years ago in 1974, and is currently funded by 27 member states. An integral part of EMBL, EMBL-EBI has 25 years of experience in ensuring continuity of access to public infrastructure and data. EMBL-EBI manages the graceful retirement of public data services as part of its portfolio management, exemplified by the retirement of ArrayExpress archive, which has been seamlessly superseded by the BioStudies database in 2021.

Europe PMC is an archive. It aggregates, preserves, and enriches content posted or published elsewhere. The majority of the content in Europe PMC is available via partner databases and open infrastructure providers, including MEDLINE, PMC, Agricola, Crossref, and many others. The data that enriches this content includes text-mined annotations, grant information for Europe PMC funders, links to external resources, and other value-added services. Annotations are in W3 annotations format and external links are in Scholix format and are available via APIs. An end of life deposit of the available annotations and external links could be deposited to a repository for preservation.

Europe PMC’s partnership with PMC USA ensures that if Europe PMC was to wind down, the existing abstracts and PMC full text content (including author manuscripts supported by Europe PMC funders) would still exist in another location, as demonstrated by the retirement of PMC Canada. The full text Preprints available in Europe PMC but not elsewhere would be made available as an end of life deposit to a repository for preservation.

🟢 Formal incentives to fulfil mission & wind-down

Infrastructures exist for a specific purpose and that purpose can be radically simplified or even rendered unnecessary by technological or social change. If it is possible the organisation (and staff) should have direct incentives to deliver on the mission and wind down.

As mentioned above, EMBL-EBI has experience and a history of responding where the community needs change.

Europe PMC is the repository of choice for its 34 funders, enabling their researchers to self-archive their author accepted manuscripts to comply with the funders’ Open Access policies. The landscape of Open Access publishing is changing (driven, for example, by the Plan S initiative). The need for Europe PMC is continually tested through the 5-year cycle of grant renewal and continuous monitoring of use. As Europe PMC is hosted by the EMBL-EBI as part of a portfolio of data services, its lifecycle is managed in the same way as resources, such as BioStudies, Ensembl, Uniprot and many others.

Sustainability

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

Day to day operations should be supported by day to day sustainable revenue sources. Grant dependency for funding operations makes them fragile and more easily distracted from building core infrastructure.

Europe PMC is funded by a combination of a grant (contributed to by 34 funders) and EMBL-EBI support. It has been running for 15 years and has grant funding secured until 2026. As a general rule, EMBL-EBI supports the core infrastructure and the grant supports both the maintenance of Europe PMC services and the development of new ones. Further project-specific grants may fund aligned developments that enrich Europe PMC, but the main Europe PMC service is not dependent on these for its core service delivery.

🔴 Goal to create surplus

Organisations which define sustainability based merely on recovering costs are brittle and stagnant. It is not enough to merely survive, it has to be able to adapt and change. To weather economic, social and technological volatility, they need financial resources beyond immediate operating costs.

As a publicly funded service, Europe PMC does not create surplus funds. Rather, Europe PMC’s resilience is ensured in the broader context of EMBL-EBI and EMBL.

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

A high priority should be generating a contingency fund that can support a complete, orderly wind down (12 months in most cases). This fund should be separate from those allocated to covering operating risk and investment in development.

As described above, EMBL’s commitment to Europe PMC effectively provides contingency but not in the form of a specific 12-month fund.

🟢 Mission-consistent revenue

Potential revenue sources should be considered for consistency with the organisational mission and not run counter to the aims of the organisation.

Europe PMC sits within the wider open data mission of EMBL-EBI. In that context, there are processes that assess grant applications to provide assurance that they are aligned with the organisational and resource missions.

🟢 Revenue based on services, not data

Data related to the running of the research enterprise should be a community property. Appropriate revenue sources might include value-added services, consulting, API Service Level Agreements or membership fees.

Europe PMC does not charge for use. A 2021 impact report by independent consultancy Charles Beagrie Ltd and 2019 report by Technopolis found that EMBL-EBI open data resources, of which Europe PMC is one, offer exceptional value for money.

Insurance

🟡 Open source

All software required to run the infrastructure should be available under an open source license. This does not include other software that may be involved with running the organisation.

Only part of Europe PMC’s software is open source. Some parts of Europe PMC’s software dates back 20 years. As Europe PMC components are refactored and replaced over time, they are typically replaced with open source software. For example, since 2019, the Europe PMC plus manuscript submission system has been developed using PubSweet, a free, open source framework developed in collaboration with the Collaborative Knowledge Foundation (Coko) and community partners, including eLife and Hindawi.

All of Europe PMC’s open source software is available via Europe PMC’s public-projects Gitlab repository.

In December 2021 EMBL released its internal policy on open science and open access which states:

“EMBL expects all of the above types of software to be Open Source by default in both services and research, and made available in open/community software repositories.”

Europe PMC is committed to increasingly making its software open source.

🟢 Open data (within constraints of privacy laws)

For an infrastructure to be forked it will be necessary to replicate all relevant data. The CC0 waiver is best practice in making data legally available. Privacy and data protection laws will limit the extent to which this is possible.

EMBL-EBI has at its core a mission to deliver open data. EMBL-EBI’s principles of service provision state:

“Our data and tools are freely available, without restriction. The only exception is potentially identifiable human genetic information, for which access depends on research consent agreements.”

A public executive summary and further details for licensing of EMBL-EBI data resources is available on the EMBL-EBI webpage. Details on general copyright restrictions are available for Europe PMC because some content is protected by publisher copyright statements. Articles and other material in Europe PMC usually contain an explicit copyright statement.

🟢 Available data (within constraints of privacy laws)

It is not enough that the data be made “open” if there is not a practical way to actually obtain it. Underlying data should be made easily available via periodic data dumps.

Article, grant and annotations metadata in Europe PMC can be accessed freely with no registration requirement for the use of the website, APIs and the bulk download via FTP. Europe PMC provides an open access subset of full-text articles and COVID-19 preprints with more permissive Creative Commons type licenses (or similar), which is available using the APIs or as bulk downloads.

🟡 Patent non-assertion

The organisation should commit to a patent non-assertion covenant. The organisation may obtain patents to protect its own operations, but not use them to prevent the community from replicating the infrastructure.

Europe PMC does not hold any patents and we can not foresee any circumstances under which we would apply for one. In the event that we did need to apply for a patent, we would be willing to issue a patent non-assertion covenant to assure stakeholders and the community that we would not use a patent to prevent the community from using Europe PMC code or infrastructure.

Conclusion

As seen in the self-audit above, Europe PMC is committed to providing open data supported by high quality, sustainable, open and community driven infrastructure. This audit demonstrates some areas in which Europe PMC could improve, for example increasing our open source code proportion. However, it would be valuable to work with the POSI authors and other infrastructure providers in the community to revise and adapt POSI to ensure it is appropriate for publicly funded services and organisations.

EDCTP joins Europe PMC funders group

2022-02-15T09:20:00.012+00:00

We're delighted to announce that the European & Developing Countries Clinical Trials Partnership (EDCTP) joins Europe PMC as a new funder. This brings the Europe PMC funder family to 34 members.

EDCTP is a public-public partnership between countries in Europe and sub-Saharan Africa, supported by the European Union. EDCTP exists to accelerate the clinical development of new or improved medicinal products for the identification, treatment and prevention of poverty-related infectious diseases, including (re-)emerging diseases. EDCTP’s approach integrates support for research with the development of clinical research capacity in sub-Saharan Africa.

Researchers funded by EDCTP will join thousands of others who make their published research articles freely available from Europe PMC as soon as possible, and in any event within six months of publication. If your research is funded by EDCTP you can submit your published manuscript for inclusion in Europe PMC via Europe PMC plus manuscript submission system.

Join us on March 16 for a webinar on “Making EDCTP-funded research open with Europe PMC plus” to learn more about the EDCTP open access policy and using Europe PMC plus to deposit research manuscripts, as well as the benefits of including publications in Europe PMC for authors and readers.

Reaching out to researchers: new Community Outreach Officer at Europe PMC

2022-02-07T10:12:00.003+00:00

Imagine you’re a life science researcher, diving into the literature to better understand your field. What challenges do you find? What tools do you wish you had?

As a researcher one faces many challenges, and one of the lesser talked about difficulties is navigating the published literature. My personal goal is to make literature research easier by showcasing all of the innovative features that Europe PMC has to offer.

I am Summer Rosonovski and I am the newest addition to the Europe PMC team. As the new Community Outreach Officer I will focus on reaching out to researchers, helping them explore Europe PMC tools and services. Europe PMC is an open, transparent, and community driven platform. Naturally, my values align with those of Europe PMC. I believe that Europe PMC keeps accessibility and open science at its heart and is an excellent resource for anyone interested in life sciences research. In my new role I will provide training on the different ways in which Europe PMC can be used to find relevant research. I will be the point of contact to support users, connect with researchers on social media and lend an ear to those sharing their feedback.

I have recently submitted my PhD thesis in Chemical Biology, investigating DNA’s mysterious structure, the i-motif. During this time I had multiple opportunities to present my research at scientific conferences, where I designed and presented award winning posters and presentations. My PhD gave me the opportunity to gain experience in training other researchers, as well as hone my science communication skills.

Throughout my time as a PhD researcher I proactively sought out a multitude of science communication activities, as I believe in the accessibility of science for all. I have experience in organising and running outreach events, such as the Pint of Science, Norwich 2020. For the general public at the Norwich Science Festival 2021 I designed and presented an online talk explaining ‘What is DNA?’. This included an interactive session to find the criminal using DNA analysis and an activity to make candy DNA models that could be followed at home. I have explored the accessibility of science through a thought-provoking guest blog piece for HelloBio ‘Walking With “Them”: The Academic Elites’. If you’re wanting to know more about me, check out my website or follow @SRosonovski on Twitter.

A screenshot of Summer’s Norwich Science Festival talk ‘What is DNA?’ from YouTube.

In the coming weeks and months you will be hearing much more from me, as I interact with the Europe PMC user community.

I would love to hear from you, learn more about potential road locks when searching for literature, and gather ideas on how Europe PMC can support your literature dive! E-mail us at helpdesk@europepmc.org, or connect with us via Twitter @EuropePMC_news to share your experiences using Europe PMC.

We look forward to hearing from you!

Europe PMC in 2021: a year in review

2022-01-20T11:11:00.000+00:00

The year 2021 has been difficult for many people working remotely, including those here at Europe PMC. We have been unable to meet in person with the users and the wider community that drives this service.

As this year has drawn to an end we have taken the time to reflect on some of the improvements made to Europe PMC to make the life science research even more accessible, discoverable, and re-usable.

Content enhancement

Europe PMC continually strives to enhance the available content in line with what its users need. To address this in 2021 we focused on increasing transparency for preprints. Preprints are an excellent open resource for researchers to rapidly share scientific discoveries before journal-organised peer review. In some circumstances authors may wish to withdraw or remove their preprint. Europe PMC now provides a way to search and display withdrawn and removed preprints with appropriate labels, for the COVID-19 full text preprint subset. Currently withdrawn and removed preprints are identified in Europe PMC using a semi-automated approach, however we hope that in the future preprint servers will be able to share the preprint withdrawal/removal status as part of the machine readable metadata freely available in Crossref.

As part of Europe PMC’s commitment to open access research, over 14,000 psychological sciences preprints from PsyArXiv were added to the Europe PMC database, making the latest psychology research more accessible and discoverable.

Following the initiative to include full text COVID-19 preprints in Europe PMC since June 2020, we have continually ingested new content and are excited to announce there are now ~27,000 COVID-19 full text preprints available for search and display in Europe PMC.

We have also expanded the amount of grant—article links available on Europe PMC by adding funding data provided by publishers to Crossref. Thus improving transparency for research funding and making it easier for funders to track publications they have supported.

Service for users

We know that keeping up to date with the literature is a time-consuming process, and based on user requests we have introduced email alerts. This feature can help users keep up with current research in their field, track new publications and preprints from over 25 different platforms, and follow individual researchers, groups, and institutions, as well as journals of interest.

For those using Europe PMC APIs we have developed a status update change module that allows users to submit batches of article IDs to identify if any articles have been retracted. For preprints this feature allows users to identify if a preprint has a new version, has been withdrawn, or has been published in a peer-reviewed journal.

In 2019 the Europe PMC article and search pages were redesigned based on several user research studies. Further improvements were made in 2021, including a redesign of the Home, About, and Help pages to address common questions that the new users had about what Europe PMC is and what it offers.

With accessibility at the heart of Europe PMC, further design changes were made to ensure life sciences research can be accessed by anyone and everyone. This year we made multiple improvements to the Europe PMC website to meet UK and US government accessibility guidelines set out by the W3C. These improvements allow those using voice commands, screen readers, keyboard commands, zooming, and other assistive devices to use the website more easily. There are a variety of browser settings that can be changed to make reading content easier, including zooming up to 300% without text spilling off the screen, changing text size, contrast, colour, and fonts, making content easier to read.

We have made it even easier for the authors supported by Europe PMC funders to link their grants to articles to meet funding requirements. During the manuscript submission process in Europe PMC plus we have introduced a grant-linking step for full text articles already available in Europe PMC.

From 1st January 2021, authors supported by Horizon Europe grants or grants from cOAlition S funders are required to release their manuscripts immediately with no embargo and a CC-BY license. We made changes to Europe PMC plus to ensure authors archiving their manuscripts in Europe PMC could comply with these new open access policy requirements.

Integrated research data

In 2021 Europe PMC has partnered with two open community databases, PGS Catalog and Xenbase, to link publications with relevant curated data records. The Polygenic Score (PGS) Catalog is an open database of polygenic scores and the relevant metadata required for accurate application and evaluation of results. Xenbase is a web-accessible resource for integrated biological and genomic data for the Xenopus model organism. Europe PMC provides access to over 53,000 Xenopus-related and over 250 PGS-related publications with links to data citing the publication discoverable from the publication Data tab.

To aid the identification of the key COVID-19 papers, Europe PMC has partnered with the Swiss Institute of Bioinformatics Text Mining team to add the Coronavirus Vocabulary (COVoc) annotations based on an ontology developed by the EMBL-EBI SPOT team. This enables searches for publications in Europe PMC that contain COVID-19 ontology terms.

In a joint project between the Europe PMC and MGnify teams, Dr Maaly Nassar’s machine learning framework enriched publications in Europe PMC with metagenomics annotations. In total the framework identifies 16 different entities that describe biome origin and metagenomics methods, such as ‘Sample Material’, ‘Body-site’, ‘Kit’, ‘Primer’ and environment ‘State’. Those same annotations can be explored in the MGnify database, with the context for each term provided as a text snippet linked to the publication.

User community

We were delighted that the Europe PMC funding was renewed for the period 2021–2026. The grant is supported by 33 international biomedical funders and is essential for the continued development and maintenance of Europe PMC’s infrastructure.

Excitingly, Europe PMC has welcomed two new funders to the funder family in 2021: the Netherlands Organisation for Scientific Research (NWO) and ZonMw. NWO funds interdisciplinary research focused on societal challenges and, as part of their commitment to open science, they also invest in research infrastructure. ZonMw funds healthcare research, with a focus on innovation, increasing scientific knowledge, and implementing these innovations and discoveries in policies and health care practices. ZonMw is an advocate for international collaboration and works closely with NWO.

The API use case page showcases projects from the Europe PMC web service user community. A new case study from the University of Virginia highlights the use of the Europe PMC REST API to study open access publishing at their institution. Using the University of Virginia's open source code and the Articles API provided by Europe PMC anyone can apply this approach to visualise the open access practices at their own institution.

The proportion of open access versus subscription-only articles published by the UVA Health affiliated authors and indexed in Europe PMC. Visualisation created using Europe PMC API and Streamlit.

This year we have created and delivered multiple webinars and training to support users and highlight the benefits of open science. The key webinars and training to highlight are:

Final remarks

Europe PMC is dedicated to continually addressing the needs of users and is proud of the new developments that have been implemented in 2021. If you are interested to find out what we are planning for 2022 please look at Europe PMC’s Roadmap and let us know what you think.

Transparency for preprints: handling withdrawals and removals

2021-12-01T09:54:00.002+00:00

Part of the appeal of preprints is the ability to post new versions, allowing researchers to continuously improve their manuscript and correct it if needed. However, in some cases the data or its interpretation presented in the preprint may be proven incorrect with time. In such cases the authors may wish to withdraw or remove the preprint, rather than posting another version. There could also be instances where preprints are removed for legal reasons, due to authorship disputes, or even as a result of erroneous posting.

Currently, there are several different ways in which preprint platforms handle such scenarios. In the case of a withdrawal the preprint itself is often still accessible, but it is supplemented with a new version containing a withdrawal notice, which explains that the preprint should not be considered part of the scientific record. This is akin to retractions for peer reviewed journal articles. On the other hand, in the case of a removal all preprint versions are removed and the content is no longer accessible, in some cases with a removal notice replacing the preprint itself. You can see the list of different withdrawal/removal policies in the ASAPbio Preprint Server Directory.

For an archive, such as Europe PMC, it is crucial to follow best practices for handling preprint metadata to enable transparency and build trust in preprints. As a proof-of-concept we now provide a way to search and display withdrawn and removed preprints with appropriate labels for the COVID-19 full text preprint subset. We identify preprint withdrawal or removal notices based on document length (notices are often just a single sentence long) using the Europe PMC plus submission system. Those records are then flagged, manually checked and tagged with the appropriate withdrawal or removal article-type [Hamelers A, Parkin M. A full text collection of COVID-19 preprints in Europe PMC using JATS XML].

Withdrawn and removed COVID-19 full text preprints in Europe PMC can be found using PUB_TYPE:"preprint-withdrawal" and PUB_TYPE:"preprint-removal" searches, respectively. Information about preprint withdrawals and removals can also be obtained programmatically, with an option to retrieve preprint status changes via the new status update search module of the Europe PMC Articles API.

A screenshot of search results for PUB_TYPE:"preprint-withdrawal" demonstrates that, to date, there are 34 full text COVID-19 related preprints in Europe PMC that have been withdrawn from the corresponding preprint platform.

Such records are clearly labeled on the preprint page with a link back to the preprint server for more information.

Examples of a withdrawn (left) and removed (right) full-text COVID-19 preprint record in Europe PMC.

A notice is also displayed on earlier versions, with the exception of preprints from servers that use a single DOI for all versions and overwrite the metadata (e.g. medRxiv and bioRxiv). In such cases a withdrawal notice replaces the preprint record.

Example of the notification for an earlier version of a full-text COVID-19 preprint in Europe PMC, where a later version is a withdrawal notice.

While the permanence of preprint records is important to support the legitimacy of preprints as scholarly outputs, in some cases preprints are removed entirely, with the preprint URL leading to a 404 page without a notification present. In such cases, removed preprints are deleted from Europe PMC as well.

Ideally, all withdrawn or removed preprints in Europe PMC, including those that we do not have the full text for, should be clearly identified, stating the reason for the withdrawal. However, currently there is no straightforward way to retrieve this information for preprints posted on different platforms. We rely on manual analysis of the flagged preprint full text to discover that it contains a removal or withdrawal notice, with a follow-up manual check on the preprint server. In the future, we hope that preprint servers will share the withdrawal/removal status in a machine readable format, potentially through a single service, such as Crossref, which would allow us and other providers to automate updates to the preprint record.

Alerts for topics, authors, preprints, and more

2021-11-11T12:36:00.000+00:00

Keeping up with the current published research has long been a challenging task. With preprints added to the mix, research is shared much quicker, extending the reading list and fuelling information overload.

There is a need for useful tools to help researchers stay on top of the new discoveries that are most relevant to their field. Europe PMC now offers a new alerts feature for keyword searches.

How can alerts help track relevant research?

Researchers can create email alerts for saved searches, to discover new articles on a topic of interest. Europe PMC alerts can help you:

track preprints from over 20 different preprint platforms;
track research articles or reviews;
track individual researchers, research groups, or institutions;
track journals that publish research in your field, etc.

How does an alert work?

When creating an alert you will be asked to sign in with an ORCID, Twitter, or Europe PMC/Europe PMC plus account. You can access all of your saved alerts from your account. Alerts can be modified or deleted at any time.

Example of saved alerts in a user account.

The Save & create alert form can be accessed via the Save & create alert button next to the search bar. Alert settings options include:

- You can edit your search and test the new search terms.

- You can edit the name of the alert.

- You can choose to receive regular email updates or to save the search to run yourself at any time.

- You can select the frequency option from as soon as available, weekly, or monthly. You will need to select a preferred day for weekly and monthly alerts. Any new results are emailed at approx. 06:00 GMT.

- You can opt to receive a partial abstract with the first few lines included in the email.

When receiving an email for your alert, it will include the title, author(s), journal information and a few lines of the abstract, if selected, for up to 25 new results, with an option to view all new results on Europe PMC if more items are found.

Example of an alert email for (bacteriophage) search on Europe PMC.

We hope that the new alerts feature for Europe PMC will make it easy to find the relevant information and stay on top of published and preprinted research. If you have any feedback regarding the email alerts please let us know via helpdesk@europepmc.org.

Using the Europe PMC REST API to Study Open Access Publishing at the University of Virginia

2021-10-25T09:00:00.000+01:00

In May 2021, the University of Virginia Faculty Senate passed a set of Open Access Guidelines and Recommendations. This was the first university-wide resolution on the subject, though the School of Data Science adopted its own open access policy a few months earlier. At the Claude Moore Health Sciences Library, we primarily serve the School of Medicine, the School of Nursing, and the Medical Center (collectively known as UVA Health). Though we now knew that the majority of the university’s faculty supported open access, we wanted to learn more about the attitudes of our library’s constituents in the health sciences.

We decided to create a dashboard to visualize what proportion of recent journal articles published by UVA Health authors were open access. This would help us to better understand the current publication landscape as well as identify particular authors who consistently published in open access journals, and therefore might be worth contacting as potential partners for outreach on the topic. UVA has institutional subscriptions to commercial software that measures research impact but the license terms for those products restrict how their data can be shared, which would limit the possibilities for future development of our project. To align with the larger project’s goal of encouraging open behaviours, we wanted to create the dashboard using only open data sources. Additionally, using open data sources and sharing our code would allow anyone to replicate it or adapt it to study their own institution’s publications.

To restrict our search to UVA Health authors, we needed an API that included institutional affiliation for all authors. We initially considered other options however the Europe PMC API proved to be the best data source for this project as it focuses on biomedical publications and the core metadata option for the API includes the institutional affiliation for all authors separated into individual fields.

After deciding on a data source, we needed to find a way to process and visualize the data. We ingested the Europe PMC API core metadata in JSON into a pandas dataframe and used Streamlit to create the visualization. Streamlit is an open source Python library which can be used to create interactive web applications. The free Sharing option allows users to create up to three complete web apps with shareable URLs using code stored in a public GitHub repository. With only three files, one for infrastructure, one for python libraries, and one for code, users can configure the environment for diverse analysis projects. We used Streamlit’s built-in caching feature to improve the speed of the application and Altair data visualization tools to create the charts.

The Open Data Dashboard now shows the proportion of open access versus subscription-only articles published by UVA-affiliated authors and indexed in Europe PMC from 2017 to the present, and we have also added an exploratory data analysis widget made using the Python library Sweetviz to provide a quick visualization of the dataset and help us uncover potential areas for future analysis.

We wanted to use the Europe PMC affiliation data to sort articles published by members of different departments or units at UVA Health, but this has proved challenging as the names are written in varying ways. Because of these risks, we have not drilled down in to the data based on department, even though this use of the data would likely be of the greatest interest to the library’s constituents.

We received assistance from numerous sources while working on this project. When we initially encountered problems in getting the full data set to load, Dr. Maaly Nassar quickly replied to our email to the Europe PMC Developer Forum and provided a piece of code which solved our problem. James Bennett at our local Code for America team recommended Sweetviz, and Randy Zwitch from Streamlit was available on Twitter for assistance setting up caching. More information on the project can be found in this blog post and our GitHub repository is available here.

Please direct any questions on the Open Data Dashboard to:

Lucy Carr Jones (lgc3t[at]virginia.edu), MSIS, Library Assistant, University of Virginia Claude Moore Health Sciences Library; and Anson Parker (adp6j[at]virginia.edu), Web Developer, University of Virginia Claude Moore Health Sciences Library.

COVID-19 grants: who, where and how much?

2021-07-26T09:57:00.010+01:00

Along with life science publications, Europe PMC offers a way to search through biomedical grants from Europe PMC funders using the Grant Finder tool. Last year, Europe PMC partnered with the Medical Research Council (MRC), the UK Collaborative on Development Research (UKCDR) and the Global Research Collaboration for Infectious Disease Preparedness (GLoPID-R), to extend its search to include COVID-19 grant data from other funding organisations.

COVID-19 grant data is retrieved monthly from the COVID-19 Research Project Tracker - a live database of funded research projects across the world related to the current COVID-19 pandemic. It is one of the most comprehensive databases, covering a wide breadth of research disciplines.

All grant information in Europe PMC is stored in a dedicated grants database, in a machine readable format. Data can be programmatically accessed using the Europe PMC GRIST API, enabling large scale analyses of the funding landscape. To demonstrate how the grant data can be used, we have gathered some insights regarding COVID-19 funding.

As of 10.06.2021, Europe PMC has funding information for 8839 COVID-19 grants awarded to 8193 distinct PIs (Principal Investigators). This includes grants for research on coronavirus epidemiology and virology, as well as grant awards in other relevant disciplines. In the latter case, funders such as ERC provide us with a curated list of COVID-19 related awards.

COVID-19 grants are awarded by 146 international funders, indicating that the current pandemic truly is a world-wide issue. You can see the geographical distribution of the funding organisations on the map below. Circle size correlates with the number of funders based within a selected country. Funders that could not be assigned a geographical location, which accounts for 23 funding organisations, are not represented on the map. This includes international and intergovernmental organisations.

The data shows that ~2% of all COVID-19 grants (168 of 8839 total) are jointly supported by two or more funder.

Altogether COVID-19 grant awards amount to at least $3.9 billion (monetary value is not available for 2500 (28%) of the COVID-19 grant records). Note that grants have been awarded in 20 different currencies which we have converted to USD for this calculation. The mean average COVID-19 grant award value is ~$615,000, which is still nearly a third lower than the average value of grants awarded by Europe PMC funders (~$845,000). This could be a result of COVID-19 grants being awarded with a shorter duration than the average funding call duration for Europe PMC funder grants. Looking at grants that have both start and end dates available, the average COVID-19 grant has a duration of 30 months, compared to 40 months for regular Europe PMC funding calls, representing a similar annual value (~$235,000 for COVID-19 grants and ~$247,000 for non-COVID-19). Another explanation may be that the most common discipline in the COVID-19 tracker is social sciences, where research costs are typically lower than in the medical sciences.

These are just some examples of what we can infer from the funding information available in Europe PMC. We hope that making grant data available via an open API in a structured form will lead to more insights by other research teams in the future.

Please note that we feature examples from our programmatic users on the Europe PMC API Case Studies page. If you have used the Europe PMC GRIST API and would like to share your story please get in touch via helpdesk@europepmc.org.

PsyArXiv preprints now indexed in Europe PMC

2021-05-11T10:00:00.001+01:00

PsyArXiv preprints are now discoverable in Europe PMC alongside peer-reviewed research

PsyArXiv’s collection of more than 14,000 psychological sciences preprints has now been indexed in Europe PMC, an open science platform that enables access to a worldwide collection of 38.6 million life science publications and preprints.

“Indexing PsyArXiv in Europe PMC means that psychological preprints will now be more discoverable than ever before. PsyArXiv users will benefit from the increased audience for their work.” - Katherine S. Corker, executive officer for the Society for the Improvement of Psychological Science, and Associate Professor at Grand Valley State University.

Since 2018, Europe PMC has indexed nearly 290,000 preprints alongside its collection of peer-reviewed journal articles. Similar to other records in Europe PMC, these preprints are linked to underlying data, journal published articles, preprint citations, comments or open peer reviews, and can be claimed to ORCID.

"We’ve seen an impressive rise in preprint popularity in the life sciences in the last few years – it’s a great way to rapidly communicate research results. [...] We hope that including preprint abstracts into Europe PMC search results, will not only enhance their discoverability, but also provide a community platform to explore some open questions.” - Johanna McEntyre, the Associate Director of EMBL-EBI Services and Principal Investigator for Europe PMC.

If you are interested to learn more about PsyArXiv preprints in Europe PMC, please register to join our live demo at 13:00 (GMT+1) on May 25th.

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About PsyArxiv

PsyArXiv (psychology archive) is designed to facilitate rapid dissemination of psychological research. PsyArXiv is a creation of the Society for the Improvement of Psychological Science (SIPS) and is hosted by the Center for Open Science (COS).

PsyArXiv allows scholars to post documents such as working papers, unpublished work, and articles under review (preprints), making them accessible to other researchers and to the public at no cost. Users can also upload revisions of their posted document and supplemental documents such as appendices.

About Europe PMC

Europe PMC is an open database of life science publications and preprints from trusted sources around the globe. Europe PMC supports the research community by supporting innovation in publishing, fostering reproducible science, and enabling data-driven discovery. Europe PMC’s mission is to build open, full text scientific literature resources and support innovation by engaging users, enabling contributors, and integrating related research data.

Over 15,300 full text COVID-19 now available in Europe PMC

2021-02-09T10:35:00.009+00:00

In July 2020, Europe PMC began indexing the full text of COVID-19 preprints. The initiative supported by Wellcome, the UK Medical Research Council, and Swiss National Science Foundation, has now made over 15,300 full text COVID-19 preprints searchable and free to read, alongside peer reviewed articles.

Number of full text COVID-19 preprints in Europe PMC by month.

Researchers can benefit from a greater number of results being returned for each query since Europe PMC search tool searches not only the abstracts but also the full text of articles and preprints. The full text of COVID-19 preprints are available for reading and reuse via a standard XML format, so if a preprint has an open license, it can be text mined programmatically, allowing deeper analysis of the COVID-19 literature.

Which servers are indexed?

Europe PMC currently indexes full text COVID-19 preprints from biomedical servers bioRxiv, and MedRxiv. Adding to this, Europe PMC also includes full text COVID-19 preprints from Research Square, ChemRxiv, SSRN and from arXiv.

Preprint server
Disciplinary scope
arXiv
Multiple scientific fields, including quantitative biology
bioRxiv
Broad life & biomedical research (from animal behaviour and cognition to zoology)
ChemRxiv
Subject-specific, including biological and medicinal chemistry
medRxiv
Broad medical, clinical and related health sciences
Research Square
All scientific fields
SSRN
Multiple scientific fields including applied sciences, health sciences, life sciences, social sciences
Disciplinary scope was taken from ‘Preprint server directory’ at https://asapbio.org/preprint-servers

Europe PMC uses the PDF freely available on these preprint servers to create the full-text HTML version of the preprint, which is later sent for author approval to display by Europe PMC. A single query will access 15,000 preprints from across these 6 servers.

Number of full text COVID-19 preprints in Europe PMC by preprint server.

Data re-use

One of the aims of the project is to provide a unique corpus of COVID-19 research for current and future research. The COVID-19 full text articles in Europe PMC have already been used for data analysis in the following studies:

Schwab, S. and Held, L. (2020), Science after Covid‐19: Faster, better, stronger?. Significance, 17: 8-9. https://doi.org/10.1111/1740-9713.01415
Fraser, Nicholas; Kramer, Bianca (2020): covid19_preprints. figshare. Software. https://doi.org/10.6084/m9.figshare.12033672.v41
Ivanova, Y., Karapeev, G., Butler, D., Gadegaard, N., Aitchison, I., Cannon, P., & Keith, N. (2020, November 29). Fluctuations in SDG relevant research output in response to COVID-19. Retrieved from osf.io/ea37y

Future plans

Europe PMC is planning to index full text preprints from Preprints.org, Authorea and other preprint servers and platforms which include relevant COVID-19 content. To see an updated list of preprint servers check the ‘About preprint page’ on Europe PMC website.

For more information about preprints in Europe PMC, visit our website: https://europepmc.org/Preprints

Europe PMC announces renewed funding and two new funders join the family

2021-01-19T09:00:00.002+00:00

Europe PMC infrastructure grant renewal

We start 2021 with the exciting news that the Europe PMC infrastructure grant has been renewed for the period April 2021 to March 2026. The grant award is supported by 30 international biomedical funders and led by the Principal Investigator Dr Johanna McEntyre, of the European Bioinformatics Institute (EMBL-EBI). The grant enables the continued development and maintenance of the Europe PMC infrastructure and supports the Open Access policies of the Europe PMC funders, by enabling researchers to self-archive journal articles.

"I am delighted that funding for Europe PMC is secured until 2026. This will allow Europe PMC to not only support the open access policies of the Europe PMC funders, but also provide comprehensive free and open access to research abstracts, full text and preprints. Europe PMC is a community resource, and a key part of European and global data infrastructure, providing vital links between data and articles to support open science”, said Jo McEntyre, who is also Associate Director of EMBL-EBI and Head of Literature Services.

Two national funding organisations in the Netherlands, NWO and ZonMw, join Europe PMC

We're excited to announce that the NWO and ZonMw join Europe PMC’s funder family this year.

The Netherlands Organization for Scientific Research (NWO), funds interdisciplinary, curiosity-driven research that is focused on societal challenges and also invests annually in research infrastructure. Notably, The NWO announced its Open Science fund in December 2020, a programme that will support researchers in developing, testing and implementing innovative ways of making research open.

ZonMw funds the full spectrum of healthcare research, from basic research to the implementation of new treatments, disease prevention, and health care improvements in the Netherlands, as well as contributing to international programmes. ZonMw works closely with the NWO, with their focus on healthcare research complementing NWO’s support of a wider range of scientific research areas.

Researchers funded by NWO and ZonMw will join thousands of others who make their published research articles freely available from Europe PMC as soon as possible. Both national funders are supporters of Coalition S meaning that all published research articles funded by NWO and ZonMw grants that are awarded from January 1st 2021, should be made immediately available for reading and reuse through Europe PMC, without embargo.

For more information about joining Europe PMC as a funder, visit our website: http://europepmc.org/Joining

Europe PMC in 2020: a year review

2021-01-14T09:47:00.001+00:00

The year 2020 was marked by the global COVID-19 pandemic and the Europe PMC team, like many others around the world, started to work from home. Scientific literature is at the heart of scientific research and during these extraordinary times, Europe PMC worked on improving existing services, building new features, increasing the full text content by including the full text of COVID-19 preprints and improving full text browsing, supporting text and data mining and engaging with the Europe PMC community. Despite the circumstances, 2020 was a busy year for Europe PMC, so let’s look back at the main achievements and the new features implemented in Europe PMC last year.

Service for users

2020 was a year of great partnerships! Europe PMC partnered with Scite to integrate smart citations on the Europe PMC platform. These smart citations provide the excerpt of text surrounding the citation, the section of the article in which the reference is mentioned, and indicates whether the citing study provides supporting or disputing evidence. Users can easily find smart citations in the Citations & Impact tab of the articles for which smart citations are available. Read more about smart citations in Europe PMC here.

Europe PMC also partnered with the Medical Research Council (MRC), the UK Collaborative on Development Research (UKCDR) and the Global Research Collaboration for Infectious Disease Preparedness (GLoPID-R) to make COVID-19 grant data more widely available via the Europe PMC COVID-19 grant finder. Over 2,127 grants from 27 international funders have been included. Read more here.

It is now even easier to link an article to the ORCID profile with the new ORCID claiming button implemented on the Europe PMC article page.

Europe PMC also supported researchers funded by Europe PMC funders to comply with Plan S by implementing new functionality in the Europe PMC plus manuscript submission system.

Full text searching and browsing

In 2020, Europe PMC also made improvements to preprint versions, aggregating all versions of a preprint together and displaying only the most recent versions of a preprint in the search results. Users can navigate through different preprint versions by using the preprint history menu. Read more here.

Europe PMC links preprints to the peer reviewed version of the article if it is available in Europe PMC. Last year, finding published versions of preprints was made easier by the new search functionality for preprints, the “published version” filter.

As a response to the COVID-19 pandemic, Europe PMC also implemented a COVID-19 search banner to make it easier for users to find the latest COVID-19 related articles. The yellow banner can be found on top of Europe PMC web pages.

Content enhancement

During the COVID-19 pandemic, researchers have published results rapidly, usually through preprints. In July 2020, Europe PMC supported by Wellcome in partnership with the UK Medical Research Council (MRC) and the Swiss National Science Foundation (SNSF), started to index full text COVID-19 preprints. This initiative has made over 13,000 full text COVID-19 preprints available for reading and reuse via a standard Journal Article Tag Suite (JATS) XML format, alongside peer reviewed full text articles. The preprints with an open license can also be programmatically accessed and downloaded for text mining, allowing deeper analysis of the COVID-19 research landscape. Read more about this initiative here.

Europe PMC collaborated with additional preprint servers. Preprint abstracts from Beilstein Archives, Research Square, SSRN and Authorea are now searchable in Europe PMC as well as the full text COVID-19 preprints from bioRxiv, chemRxiv, medRxiv, Research Square and SSRN.

Supporting text and data mining

Europe PMC also welcomed three new annotation providers: OntoGene, PheneBank and Metagenomics (EMERALD) which provide annotations on cell, cell lines, clinical drugs, molecular processes, organ tissues, pathway, anatomy, phenotype and metagenomics concepts. Users can now find over 1.3 billion annotations covering 42 different annotation types in Europe PMC.

SciLite annotations, the powerful tool for highlighting annotations in Europe PMC, gained a new look in 2020. The new version of SciLite includes new annotations types, a new panel interface and improved features such as the chemical and protein structure viewers that allow readers to visualise and interact with the structures directly on the article page.

User community

Early last year, Europe PMC connected with the Europe PMC API community to release an API use case page where programmatic users can share the applications they have created using Europe PMC APIs.

In March 2020, Europe PMC released a video showing how different users such as researchers, policy makers, biocurators and innovators use Europe PMC.

Europe PMC continued to run regular webinars on various aspects of Europe PMC. We appreciated the questions and feedback we received from many attendees.

“I learned about Europe PMC and the way it is connected with databases such as OMIM, ENA, InterPro, Mouse genome informatics, etc.”

“The Europe PMC is really comprehensive and fun to use”

“It was informative as I never used Europe PMC. Thanks”

Europe PMC participated in the eLife Innovation Sprint 2020 working on the projects convidpreprints.com and Annotate them all. In mid September, the team also participated in the conferences Reproducibility, Replicability and Trust in Science (RRTS20) and OASPA2020 with posters and lightning talk on ‘Full text COVID-19 preprints in Europe PMC’, ‘Connecting research resources - building the PID Graph in Europe PMC’ and ‘Global Grants DOIs in Europe PMC’.

Last November, Europe PMC open-sourced Text-annotator, a JavaScript library to locate and annotate plain text in HTML. Text annotator is used in Europe PMC to highlight article title, snippets and biological entities via SciLite annotations. Read more here. The Europe PMC team also published the article ‘Europe PMC in 2020’ giving a snapshot of what Europe PMC has to offer researchers.

Europe PMC is glad to have been able to develop and implement new features to support users' needs in 2020. The team will continue to make it easier for users to read and extract information from the scientific literature in 2021.

If you are interested to find out what we will be working on in 2021, take a look at Europe PMC’s road map and leave a comment or email us if you have questions.

Connect with us via Twitter and help to share the developments at Europe PMC in 2021. Programmatic users can subscribe to Europe PMC’s developer forum to leave questions.

Research Square’s Full-text COVID-19 Preprints Now Indexed in Europe PMC

2021-01-12T14:25:00.008+00:00

More than 4,500 Research Square preprints discoverable alongside peer-reviewed research

Research Square’s collection of more than 4,500 full-text COVID-19 preprints have been indexed in Europe PMC, an open-access repository of more than 1 million biomedical research works.

The overall effort, jointly supported by Wellcome, the UK Medical Research Council, and Swiss National Science Foundation, expands Europe PMC’s collection of more than 13,000 full-text COVID-19 preprinted research manuscripts in HTML format, and it allows the research community greater access to this COVID-19 research.

“COVID-19 has connected science and publishing in unprecedented ways, and the urgent need to share research immediately has fueled an important need for preprints,” said Michele Avissar-Whiting, Research Square Editor in Chief. “Europe PMC is doing an excellent job of fulfilling scientists’ needs through its full-text repository of preprinted COVID-19 research.”

Since 2018, Europe PMC has indexed more than 200,000 preprints alongside its collection of peer-reviewed and journal-published articles. Similar to other articles in Europe PMC, these preprints are linked to data behind the paper, can be claimed to an ORCID, included in citation networks, and linked to comments or open peer reviews.

"Being able to access full-text preprints and peer-reviewed articles on COVID-19 in one place, and within the context of related life-sciences publications, will provide better support for research in this area", said Jo McEntyre, Associate Director of EMBL-EBI and Head of Literature Services.

_________________________________________________________________________________________

About Research Square

Research Square, a division of Research Square Company, exists to make research communication faster, fairer, and more useful. Our industry-leading preprint platform, launched in 2018, is a large, author-centric preprint server that brings transparency to the peer review process. Through our journal-integrated In Review service, innovative author dashboard, manuscript assessments, and research promotion services, we enable researchers to establish the primacy of their work, share it with the broader community, and receive useful feedback much earlier in the publication process. By improving the way science is shared, we accelerate the pace of global discovery and advancement.

For more information on our platform and research promotion services, visit researchsquare.com.

Contact: Phillip Bogdan, Communications Manager

phillip.bogdan@researchsquare.com

About Europe PMC

Europe PMC provides comprehensive access to trusted sources of biomedical literature, all available in a single search, by indexing the metadata and abstracts of about 38 million journal published articles, reviews, preprints, micropublications, books, patents, and guidelines. Europe PMC supports the research community by developing tools for knowledge discovery, linking publications with underlying research data, and building infrastructure to support text and data mining. The Europe PMC goal is to create a supportive environment around open access content and data, to maximise its reuse.

Contact: Europe PMC helpdesk

+44 (0) 1223 49 41 18

helpdesk@europepmc.org

Source press announcement: Research Square’s Full-text COVID-19 Preprints Now Indexed in Europe PMC

Enriching Europe PMC publications with Metagenomics annotations

2020-11-11T10:30:00.003+00:00

We are excited to announce the recent release of metagenomics annotations for Europe PMC publications. Thanks to the machine learning framework of Dr. Maaly Nassar for the joint EMERALD project between Europe PMC and MGnify teams, recognising metagenomics key terms in literature can now provide detailed biome descriptions for unravelling microbial implications in a variety of environmental-, engineered- and host-associated phenomena. Using a mixture of a literature-based machine learning (ML) and natural language processing (NLP) approaches, terms pertinent to 16 novel metagenomics concepts were identified in Europe PMC literature. Those concepts cover entities related to biome sample and origin as well as metagenomics experimental methods, and are all available in the Europe PMC annotations platform. Check the table below to learn about these concepts (annotation types) and their descriptions.

Annotation type	Description
Host	The organism where the microbiome is found
Engineered	Microbiome's man-made environment
Ecoregion	Micrbiome's natural environment
Date	Sampling date
Place	Microbiome's place or geocoordinates
Site	Microbiome's site within place
Body-site	Host body region/structure where microbiome is found
State	Host/Environment state
Sample-material	Sample from which the microbiome is extracted
Treatment	Host/Environment treatments
Kit	Nucleic acid extraction-kit
Gene	Target gene(s) (e.g. hypervariable regions of 16s/18s rRNA gene)
Primer	PCR primers
LS	Library strategy (e.g amplicon, whole metagenome)
LCM	Library construction method (e.g. paired-end, single-end)
Sequencing	Sequencing platform

Publications with the new annotations are searchable on Europe PMC using the search syntax (ANNOTATION_PROVIDER:"Metagenomics"). Entity types can be highlighted in the text of open access articles using the SciLite annotations tool.

Additionally, these annotations are available for programmatic access via Europe PMC search and annotation APIs.

Explore metagenomics annotation types in Europe PMC and give us your feedback. Want to know more about Europe PMC annotation platform? Get in touch with annotations@europepmc.org.

Announcing the new version of SciLite - the Europe PMC tool for highlighting annotations

2020-09-22T09:59:00.000+01:00

This month, Europe PMC released a new version of SciLite, a powerful tool for highlighting annotations in life sciences publications. SciLite is powered by the Europe PMC annotation platform via the open annotation API, which provides access to over 1.3 billion annotations. Highlighting annotations in the text enables users to easily scan the article and locate key biological entities, such as genes/proteins, accession numbers, protein interactions, diseases, gene-disease relationship and more.

SciLite annotations has been redesigned to improve the speed of information retrieval and assist scientists and database curators to scan articles, extract facts and evidence from the biomedical literature, as well as locate the primary data cited in a given publication. Imagine yourself being able to locate and quickly visualise a protein structure of your interest on a single page! This is how SciLite helps with speeding scientific discovery.

Annotations can be accessed via the ‘Annotations’ option on the right-hand side on the article page. Clicking on ‘Annotations’ opens a new panel and selected terms will be highlighted in the text of the article. Notice that annotations can only be highlighted on articles with an open access license.

The new SciLite version includes new annotation types, a new annotation panel interface and new features. Annotation types now include cell, cell lines, clinical drugs, molecular processes, organ tissues, pathway, anatomy and phenotype. The new panel offers easy navigation through annotations and displays a popup window with a quick link to relevant data resources.

Additionally, the new version offers a chemical structure viewer. Readers are able to visualise protein and chemical structures in the annotation panel as well as in the highlighted text.

Highlighted annotations display links to relevant database records enabling users to locate the primary data in the text by linking text mined and curated bioentities to public life sciences databases. Additionally, the new improvements include options to endorse, report errors or share the annotation via a linkback URL.

Identifying a plethora of complex biological terms and concepts in publications was made possible due to a successful partnership with a variety of text mining groups that use text mining algorithms to identify different types of biological entities, and enable text miners to showcase their work to a wider public via SciLite annotations.

Europe PMC acknowledges all the annotation providers for cooperating towards submitting their annotations and welcomes new contributions from text-mining and curation communities to share annotations via the annotations submission service. Europe PMC would also like to thank all the participants who took part in usability sessions, to test and feedback on the improvements to the Scilite Annotations tool.

Want to know more about SciLite, annotation APIs or submitting annotations? Get in touch with annotations@europepmc.org.

Europe PMC partners with UKCDR to release the Covid-19 Awards Search

2020-07-28T10:30:00.000+01:00

As a response to the current pandemic crisis, organisations worldwide have increasingly made funding available for COVID-19 research. As part of the COVID CIRCLE programme, the Medical Research Council (MRC) has worked with the UK Collaborative on Development Research (UKCDR) and the Global Research Collaboration for Infectious Disease Preparedness (GLoPID-R) to make COVID-19 grant information from international funders more widely available and accessible. This COVID-19 grant data is now searchable via Europe PMC. Europe PMC, the database of biomedical literature, supports grant search via the Grant finder tool which allows searching biomedical research grants awarded by the Europe PMC funders. To date, the initiative has resulted in inclusion in the Grant Finder of funding information for over 1,800 COVID-19 grants awarded by more than 25 funders from countries across the globe. Note that many of these grants have been jointly-funded. The grant information is accessible to website users via a 'COVID-19' tab in the grant finder tool, and can be programmatically accessed via the Europe PMC GRIST API.

The team at the MRC led by Dr Ian Viney, MRC Director of Strategic Evaluation and Impact, has been responsible retrieving the grant data from the Covid-19 Tracker as it updates and feeding it in a machine-readable format to the team behind Europe PMC to load it into the grant finder.

Dr Viney commented “It is now crucial that research organisations focus on the gaps and opportunities in the busy coronavirus research landscape. Tracking the research underway globally and in a timely fashion will allow resources to be targeted to best effect, and with the launch of the Europe PubMed Central covid-19 grant finder we now have the tools in place to keep everyone informed.”

For more information, please contact helpdesk@europepmc.org.

Europe PMC to include the full text of COVID-19 preprints

2020-06-08T13:45:00.000+01:00

In this pandemic, researchers have responded by publishing results rapidly, often through preprints.

In fact, up to half of the publications in Europe PMC on COVID-19 are preprints rather than peer-reviewed journal articles. Currently, the full text of these preprints are scattered as PDFs on preprint servers, or, available as a non-standard set of documents for machine learning purposes.

In a new project, supported by Wellcome in partnership with the UK Medical Research Council (MRC) and the Swiss National Science Foundation (SNSF), we will make the full text of COVID-19 preprints available on Europe PMC, a large and sustainable life sciences archive, for reading and reuse via a standard XML format, alongside peer reviewed full text articles.

“Being able to easily search and read preprint full text on a site already frequented by millions of users means that they will be significantly more discoverable by people, and more open to scrutiny”, says Jo McEntyre, Associate Director of EMBL-EBI and Head of Literature Services. “We will make use of existing infrastructure to integrate these COVID-19 preprints into the typical ecosystem of publications - for example, linking to the underlying data”.

This will accelerate scientific research on COVID-19, provide an opportunity to build new open and rapid publication systems, and form a corpus for future history of science research.

"The COVID-19 pandemic has the potential to be the "Napster moment" for preprints, which in turn could herald a way in which research outputs are shared in the future.  Ensuring preprints are fully discoverable and reusable will help ensure that they are treated as first class research objects.  This initiative to make them fully discoverable through the Europe PMC repository will help to realise this goal."

Said Robert Kiley, Head of Open Research at Wellcome

In the coming weeks and months, we will be engaging with preprint servers and preprint authors to make as many COVID-19 preprints as possible available for reading and reuse via Europe PMC. If you are the corresponding author on a preprint on SARS-CoV-2 or COVID-19, published on one of the major preprint platforms, we will soon be asking you to review the Europe PMC version of your work.

Europe PMC has been indexing preprint abstracts since 2018 and has the experience in managing full text workflows at large scale. A total of approximately 150K preprint abstracts currently sit among all of PubMed (31M abstracts) and 6M full text articles shared with PMC in the USA. These are XML-based workflows based on international standards (JATS). Europe PMC has played a leading role in preprint community standards development and has hands-on expertise in publication workflows that include versions across multiple sources with diverse approaches.

In addition, Europe PMC has several mechanisms to integrate related material - whether it is data behind the paper to substantiate conclusions, ORCID claiming of preprints, inclusion of preprints in citation networks, or to comments on peer review platforms, impact metrics, or links to reagents.

Jessica Polka, Executive Director of ASAPbio said:

"This exciting initiative will create a reading experience that is not only more seamless, but also potentially richer. Openly licensed documents can be text mined and enhanced with SciLite annotations, adding context for readers. The inclusion of the full text of COVID-19 preprints in Europe PMC is an important step in the integration of preprints into the scholarly communications infrastructure."

To find out more about this initiative, read the Preprints in Europe PMC page or write to Europe PMC at: helpdesk@europepmc.org.

Global grant IDs in Europe PMC

2020-06-04T09:20:00.001+01:00

In September 2019 we welcomed the first open, global grant IDs to Europe PMC. Wellcome became the first funder to register DOIs for their grant awards with Crossref. Grant metadata is provided by Europe PMC, and in a pilot integration, the grant IDs were featured in a PLOS ONE publication. This is a very exciting development that will hopefully make it easier to effectively track the impact of research funding. So what is the big news about?

What are grant IDs?

Open, global grant identifiers have been in the making for some time. Though grant numbers are already in use by many funders, they are often local and based on an internal pattern.

This might create some issues when looking up grant information provided by different funders - for a grant with a local ID 207467 two records exist in Europe PMC, one awarded by Wellcome and another by the European Research Council.

One of the proposed solutions is adoption of global grant IDs in the form of DOIs, which offer the advantages of being unique, persistent, and easy to integrate into existing systems.

To create DOIs for their grant awards funders need to follow three simple steps:

join Crossref as a member;
register associated metadata, such as grant award title, amount, currency, date, etc;
provide an openly available online resource to which the DOI would resolve - a landing page describing the grant.

Creating grant DOIs

As the first step in the process, Wellcome became a Crossref member through a new type of membership developed specifically for this purpose. It is distinct from the publisher membership and is designed for funding agencies. Upon registration Wellcome was assigned a unique DOI prefix.

DOI example for a Wellcome-supported grant.

For the second step, Europe PMC registered global grant IDs for Wellcome-funded awards with Crossref on behalf of the funding agency. Because Europe PMC already runs an open database of grant awards for all 31 Europe PMC funders, we were best placed to provide Crossref with the necessary metadata.

The metadata schema is comprehensive and allows for a detailed overview of the grant. Europe PMC presents the information registered for most of the fields, including the funding percentage for grant awards supported by multiple funders, or ORCIDs for investigators on the grant (see scheme below). The full schema and documentation are available on GitHub.

Metadata fields that Europe PMC provides to Crossref when registering a global grant ID.

Greater transparency for funding information

The beauty of a DOI is that it points to a physical location, some place where an interested user can see the details of a particular grant. For Wellcome, that place is a grant record on Europe PMC’s website. This means that the funding information becomes more transparent and can be easily linked to the research output.

Example of the grant record on the Europe PMC website. This record matches the grant DOI referenced in the PLOS ONE article below.

In a pilot effort the journal PLOS ONE coordinated with Wellcome-funded authors to include newly registered global grant IDs in the metadata of the publication. This means that the readers can now seamlessly navigate from the article to the grant record and examine the support provided by Wellcome for this particular study.

Global grant IDs for two Wellcome grants featured in the Funding section of a PLOS ONE publication. The link for the first of these Wellcome grants leads to the grant record shown in the figure above.

Notably, all of this grant-associated metadata is freely available not only on Europe PMC’s website but also programmatically, through the public GRIST API. The newly created global grant ID along with the local grant number have been incorporated into the API response. The information will also be available via Crossref’s APIs later in 2020.

Future plans

DOIs for grants have been registered on behalf of Wellcome for 237 grants awarded in 2019. Grant IDs will be assigned retrospectively to Wellcome grants awarded and registered in Europe PMC’s GRIST database from years prior to 2019. This will encompass approximately 13,500 Wellcome grants currently available in Europe PMC.

The adoption of global grant IDs also allows us to create a more interlinked PID (persistent identifier) graph - as Europe PMC hosts data for both publications and grant awards we are well-positioned to link publication DOIs with DOIs for grants, supporting better tracking of the research funding impact.

We hope that by implementing global grant IDs, grant data can be easily collected on submission by publishers and repositories and automatically fed into researcher assessment platforms, thereby simplifying researchers’ workflows.

For more information

Europe PMC funders, please contact helpdesk@europepmc.org if you’d like more information about registering grant DOIs.

For more general information from Crossref please see their website.

Europe PMC’s contribution to this work has been funded by the Europe PMC funders and the European Commission: FREYA - Connected Open Identifiers for Discovery, Access and Use of Research Resources (777523)

Preprint server	Disciplinary scope
arXiv	Multiple scientific fields, including quantitative biology
bioRxiv	Broad life & biomedical research (from animal behaviour and cognition to zoology)
ChemRxiv	Subject-specific, including biological and medicinal chemistry
medRxiv	Broad medical, clinical and related health sciences
Research Square	All scientific fields
SSRN	Multiple scientific fields including applied sciences, health sciences, life sciences, social sciences