Tuesday, 28 February 2017

Sort it out: Sorting your search results with Europe PMC


Imagine you are exploring a new topic. You start by searching for relevant papers in the field. You type your query, click the search button, and end up with thousands of scientific articles, waiting to be read. How do you identify which papers to focus on?


In Europe PMC, search results can be sorted differently to help you navigate through the literature. By default, results are sorted by relevance. But how is relevance defined? Let’s look at a search example: say we are interested in oxidative DNA damage. Once you type that string into a search box, the sorting algorithm ranks all your results and displays them in order. The algorithm takes into account how often search terms are found in the text. A document that mentions "DNA" ten times is likely to be more relevant to you than one with a single mention. The relevance score also depends on how many of the search terms a document contains. For instance, papers discussing "oxidative damage" or "DNA damage" are less appropriate than the ones specifically covering "oxidative DNA damage".
Rare terms will be more relevant than common ones. Note that we expand your search by including synonyms, so whenever you search for DNA damage, you will also discover articles mentioning genotoxic stress. You can switch off synonym expansion in the advanced search, or simply place your search terms in double quotes for an exact match, e.g. "oxidative DNA damage".



Scientific abstracts are ranked higher than articles, and papers are considered more relevant than books and other documents. Nonetheless, you can always change the type of content you are looking for via the "Popular content sets" on the right-hand side of the search results, or in the advanced search.



Using our relevance sorting, more recent publications will appear higher in the list, but if you want the latest papers over anything else, you can simply sort by date. For instance, if you are eager to see the latest manuscript from your collaborators, or the new publications from your favourite journal, just look at the most recent papers. What if, instead, you are interested in classic articles that have pioneered the field and laid the foundation for future research? Good news: you don't need to scroll to the last page of results. Simply search by date, in reverse order. Now you can see how a scientific field has progressed.



Another way to search for foundational articles is by sorting results by times cited. Citation counts can help you find experts in the field, or help you identify the most impactful works. When ordering results by times cited, the number of citations is displayed for each paper.



With Europe PMC you can find research that matters with the click of a button. Sorting has never been easier!

Tuesday, 20 December 2016

Europe PMC - a year in review

This has been a very busy and fruitful year for Europe PMC. With holidays approaching we take a look back at some of the Europe PMC achievements and milestones of 2016.
We kicked off in January with a new, mobile-friendly homepage and information pages. The final design was based on user research in which we gathered lots of feedback from you to come up with design concepts, which were thoroughly tested again before release. We still have work to do on improving these pages and we intend to chip away with making them better, based on feedback, throughout 2017.
Our spring was focussed on the migration of manuscript submission services from JISC to the EMBL-EBI. We installed a database (developed by JISC) that contains information on all the grants awarded by the funders of Europe PMC. This information is important to us to authorize the upload of manuscripts from grant holders, but we also make the data discoverable on the Europe PMC website via the grant finder, or programmatically via the GRIST API. Over 2500 grants have been added by our funders since the spring and the database now includes more than 56,000 grants, crosslinked to the articles they supported.
Summer was a hot time for us. One of the key objectives for Europe PMC is to enable application developers and text miners to reuse the open access full text content, in order to find innovative approaches to searching, filtering and reading the scientific literature. Towards this goal, in July we launched SciLite - a tool that allows text-mined terms to be displayed as an overlay on research articles. For Europe PMC users, SciLite makes it easier to scan articles for key concepts and provides deep links with related data. For text miners, it is an opportunity to showcase their work to a wider public. SciLite is based on the Web Annotation Data Model and is open to any text-mining group. So far, SciLite operates on articles with a CC-0, CC-BY or CC-BY-NC licence, and has contributions from the National Centre for Text Mining (NaCTeM) and the Bibliomics and Text Mining group at the University of Applied Sciences, Geneva, as well as from the core Europe PMC text-mining pipeline; the number of contributors is set to grow in 2017. All the full text annotations are available via a SPARQL API.
As a part of our mission to deliver a world-class service for all of our users, we took a major step towards improving our search by migrating Europe PMC indexing to Solr in the late summer. This has already significantly improved the speed with which we can return search results, as well as making our indexing of new content more efficient. As well as these basics, Solr comes with some useful features built-in, such as filters, auto-suggestions, and snippets, which we plan to start exploiting next year. Other search improvements introduced in 2016 include the addition of reverse sort orders for “date” and “times cited”, so that you can see results ranked by “oldest first” or “least cited”, and the ability to search by embargo date (as well as their display on abstract pages).
Finally, for the summer, our family of 27 funders was joined by the Academy of Medical Sciences (AMS), who became a member of Europe PMC so that the research they fund can be archived in Europe PMC, supporting their open access policies.
We are always open to new opportunities to improve on existing services. This year our External Link providers, who link out from the content in Europe PMC to their resources, can now display an image alongside the link itself. Already the iconic Altmetric donut is apparent on articles under the “External Links” tab, the CitePeer icon alerts users to alternative reference lists on the Related Articles tab, and the ImpactStory badge can be seen on the Author Profile pages. The Author Profile pages are generated for every researcher with a paper in Europe PMC listed in their ORCID profile, and their number has been constantly growing throughout the year. Currently, there are about 350,000 life science researchers actively publishing and using their ORCIDs, having claimed about 3.5 million articles available in Europe PMC.
Our autumn has been about building a program of community engagement and starting research projects with users that will inform next year’s development. The Europe PMC team has now expanded to include a community manager. We hope that this will help us to connect and reach out to all of our stakeholders, create opportunities for networking and discussions, as well as to identify useful synergies. It’s critical to us to understand the needs of our user community and their goals, and manage Europe PMC services accordingly. Finally, as part of our community engagement, we aspire to be open about our development plans in order to gain feedback at the earliest opportunity. So we have concluded this year with the publication of a roadmap that summarizes our recent accomplishments and highlights our near-term development plans, which we will update quarterly on the Europe PMC website. As always, we welcome your feedback. Leave a comment, send us an e-mail, or connect with us via Twitter.
We are looking forward to 2017 and wish all our users happy holidays. Season’s greetings from Europe PMC!

Monday, 7 November 2016

Growing connections: new Community Manager at Europe PMC

What exactly is Europe PMC? How is it different from PubMed Central? What can I do with Europe PMC?
Those are some of the questions I had myself when I first heard of Europe PMC. And now my task is to make sure that everyone can answer them easily.
My name is Maria Levchenko and I am a recent addition to the Europe PMC team. As a Community Manager I am responsible for reaching out to all of our users, informing them about new developments, but also gathering their valuable feedback, in order to make our services even more user-friendly and helpful for everyone.
My background is in biomedical research. I have also briefly worked at the European Research Council – one of the science funders that support Europe PMC – to better understand how funding agencies shape the way we do science.
My interest in Europe PMC stemmed from their goal to create a world-class literature resource. I am passionate about tools that help the scientific community on their quest for knowledge, and I believe that Europe PMC can do for research what Google does for our everyday life.
Our mission is to build open, full-text scientific literature resources and support innovation by engaging users, enabling contributors and integrating related research data. Europe PMC provides access and adds value to more than 30 million abstracts and almost 4 million full-text articles. All of the content in Europe PMC is free to read and we strongly support open access, in order to make the scientific literature available to everyone. On top of the core content, we see Europe PMC as a community-sourced platform for new developments that will improve the ways we can search, browse and integrate the literature with research data. We strive to be open about our work so that anyone can use the services and create new tools. We want to foster a sense of collaborative community, and this is where I come into play. My role is to connect with you, our users, provide you with the means to read and use the content and make your own contributions, helping to make Europe PMC a useful resource for scientists, developers and the general public alike.
In the coming weeks and months, I will be sharing news about our work, providing useful materials on how to use our service, as well as responding to your feedback.
We invite you to tell us what you think about Europe PMC and its role in your professional life. Leave a comment, send us an e-mail at helpdesk@europepmc.org, or connect with us via Twitter @EuropePMC_news.
Looking forward to hearing from you!

Friday, 9 September 2016

SciLite Annotations

Manual curation is vital for maintaining quality information in biological databases. However, with the exponential growth in biological data this approach is both challenging and time consuming. We wanted to create a scalable and sustainable process which could complement manual curation.   

We recently launched a new service - SciLite - that allows text-mined annotations to be displayed on research articles. The aim of this effort is to promote sustainability of curated databases by bridging the gap between literature and data. To this end, SciLite:
  • supports database curation processes, by highlighting biological concepts, making it easier to find key concepts described in articles;
  • provides a mechanism to link those concepts to the related resources, for efficient data integration. 
SciLite's open design enables community-driven annotations, from text-mining groups, and manual annotations, to be made available to Europe PMC users.

What are SciLite annotations?

SciLite annotations enable biological terms and concepts, such as genes/proteins, diseases, organisms and accession numbers, to be highlighted on full text articles in Europe PMC. Using the check-boxes on the right-hand side of article pages, readers can select the types of concepts that they are most interested in and matching annotations for that article will be highlighted on the article text as below. 







Clicking on the highlighted terms in the text opens a popup with a link to related database record. In the example below, an interactive Protein Data Bank (PDB) structure model is also provided when you click on a highlighted PDB accession number.


When annotations are provided by the text-mining community, the source of the annotation is displayed. In the example below, the Gene Reference into Function (GeneRIF) annotations were provided by the Text Mining group at HES-SO, Geneva, Switzerland.


Another text-mining group - NaCTeM - has provided phosphorylation event annotations, as shown below.



Take a look at this example article with annotations.
Annotations are displayed on articles with a CC-BY, CC-BY-NC or CC-0 license.

How are annotations generated?

The biological terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. Any text-mining group can participate in this scheme. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model, and stored in a triple store via the EMBL-EBI RDF Platform. If you are a text miner, find out how to provide annotations to Europe PMC at our SciLite annotations page.

We're improving annotations with your help

Because annotations are generated automatically by text mining algorithms, we want to ensure that annotations are useful to users of Europe PMC. On each annotation there is the opportunity to provide feedback by either marking the annotation as incorrect, or endorsing useful annotations.
Screenshot showing feedback feature for an annotation
This information is fed back to the Europe PMC team and will be acted upon, helping to improve the annotations overall.


Thursday, 4 August 2016

Academy of Medical Sciences joins Europe PMC

We're delighted to announce that the Academy of Medical Sciences has joined Europe PMC as a new funder, bringing the total funders to 27.

The Academy of Medical Sciences represents the diverse spectrum of medical science – from basic research through clinical application to healthcare delivery. Their mission is to promote medical science and its translation into benefits for society.

Scientists and clinicians funded by the Academy of Medical Sciences 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.

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

Tuesday, 2 August 2016

Search improvements


"Any sufficiently advanced technology is indistinguishable from magic."
- Arthur C. Clarke

Sometimes the changes we release on Europe PMC are not immediately obvious! For the last few months we've been working hard to migrate our search to a technology called Solr. Our search has been using a Lucene-based index and customised query handler for several years. It was starting to feel the strain of the increasing number of search queries on Europe PMC (we have over 1 million unique users per month), and was proving cumbersome to maintain.

Our new search using Solr may not be "magic", but it's faster, nimbler and easier to maintain. You might notice some subtle improvements including:

Increased performance

Based on our current testing, searches are on average 20 times quicker using Solr than using the previous search engine. We will continue to test and monitor the performance of Solr.

In the graph below Solr is represented by the red line and our previous search engine is represented by the blue line. You can see over a trial period that http:// requests were processed by Solr more quickly than requests to the previous search engine.

Graph showing duration of http:// requests, comparing Solr search with our previous search


Improved title searching

If you search for part, or all, of an article title using a free text search, articles which have matching titles will appear high up in your search results. It should therefore be much quicker and easier to find articles by title.

Popular content sets are quicker to load

In the past you may have noticed that the popular content set filters (which allow you to filter results by full text articles, open access, reviews, patents, books and documents) are slow to load on our search results page. With the Solr search the filters load much more quickly.

Author profiles are updated more quickly

If you have claimed articles to your ORCID record, your Europe PMC author profile will be updated more quickly than previously. Claimed articles should appear in your profile within 30 minutes, rather than within 24 hours.


The Solr search provides a strong architectural foundation for Europe PMC, which will make it easier and quicker to introduce new search features. We will announce any future developments on this blog.

If you have saved searches you may notice that the number of new results for your search seems different. That's because Solr has a different way of handling synonyms, so it is possible that you will have more, or less, articles for your search term than the previous search

If you have any feedback about the new search, please let us know using the feedback link at the bottom of the website, or by emailing helpdesk@europepmc.org.


Thursday, 9 June 2016

5 ways to use the new Grant Finder

We've recently launched a re-designed Grant Finder on Europe PMC. You can use the Grant Finder to search over 56,700 biomedical research grants, awarded to the 23,000 Principal Investigators supported by the 26 Europe PMC funders.

Learn 5 ways to use the new Grant Finder:

1. Find a collaborator

As a researcher, or student, you can find potential collaborators / PIs working in a related research area. Search for a research topic, by entering a term in the 'Keyword' field as shown in Figure 1 below. This will search the grant titles and abstracts.

Figure 1: The new Grant Finder search

2. Find funded projects in your field

If you're writing a grant application, you can use the Grant Finder to search for grants by funder, to discover which grants a funder has recently awarded, in a similar area. If you know the name of the funding stream you are applying to, enter this in the 'Keyword' field. If you know the name of a Principal Investigator in your field, or their ORCID, you can enter these details in the relevant fields.

3. Find potential funders

As a PI you can discover which smaller funders have funded research in your area. Use the 'Keyword' field to enter in a phrase describing your research area, for example a disease or protein name.

4. Find out which publications are associated with a grant

To find out what research articles have been published, you can easily link to publications associated with a grant from the search results page (or from a grant page), as shown highlighted in red below in Figure 2 and Figure 3:

Figure 2: Links to publications appear under search results as above.

Figure 3: Links to publications on a grant page

5. Find out more about the funding from a specific article

If you are searching for articles on Europe PMC, you can see which funders have supported the research, just below the abstract as shown below in Figure 4. From here you can link to the grant page to find out more details about the grant award.

Figure 4: Funding details are shown under the article abstract.

If you are interested in using our open grant data in your website or application, find out more about how to use our GRIST API.

Let us know what you think of the new Grant Finder!