University at Buffalo - The State University of New York
Skip to Content
Europe PMC Help - Europe PMC

Help using Europe PMC

Europe PMC Methods

Europe PMC Search

Europe PMC Accounts

Europe PMC Author Profiles

What can I do with my search results?

Europe PMC Content

Additional Services and Tools

General Information

Search Syntax Reference

Europe PMC Methods

How does the search work?

Europe PMC utilises Apache Solr, a high-performance, full-featured text search engine library written entirely in Java. A score is assigned to a document based on the frequency with which the search term is found. A weighting is also applied based on publication date, therefore newer documents are more likely to appear higher in the Europe PMC default relevance sort order.

Back to top

What happens when I sort by relevance?

Europe PMC displays the most relevant results for the search executed, according to document scoring and weighting. The document with the highest score is displayed first, followed by second and third highest scoring documents and so on.

See also How does the search work.

Back to top

How is text mining integrated into Europe PMC?

Text-mining is currently integrated into Europe PMC in two ways:

  • In an article's abstract you can highlight biological entities in the text using the 'Show annotations in this abstract' feature on the right of the screen. Links are provided from highlighted terms to relevant databases e.g. Uniprot.
  • In an article's full text view annotations are displayed on the right of the screen (if the article has a CC-BY, CC-BY-NC or CC-0 license). Read more about SciLite Annotations. A full view of all text-mined entities is available via the 'BioEntities' tab.

Back to top

How does Europe PMC derive its citations network?

To show citation counts for individual articles in Europe PMC requires that reference lists for as many relevant articles as possible are known, and that the citations within those reference lists can be identified uniquely, for example, by resolving to a PubMed ID. The number of "Cited By" articles listed for any individual article depends not only on the scientific importance of the article, but also on the size and scope of the dataset from which the citations have been extracted.

Why do articles in Europe PMC list fewer citations than other citation information services?

The citation dataset available to Europe PMC is based on open citation data and is smaller than those held by subscription-based services such as Web of Science or Scopus. Therefore, the number of citing articles that we show for any given Europe PMC article is likely to be comparatively smaller than the number you would see using these services. When indicated, you can link directly through to Web of Science citations (providing you, or your organisation, are subscribed to Web of Science) via the citations tab. The tab is available on both the Abstract and Full Text views of an article.


Back to top

Why is the citation information incomplete for some articles listed in the citations tab?

For complete information to be available, the references in the source article have to have sufficient information and to be sufficiently formatted for our processing to redisplay correctly.

Back to top

The BioEntities tab is available on both the Abstract and Full Text views of an article. The tab may be populated with data from one of two sources:

  • Curated database links to services such as ENA, InterPro, PDB, IntAct, ChEMBL, ChEBI and ArrayExpress.
  • Full text text-mined links including European Nucleotide Archive, UniProt, PDB, OMIM, RefSNP, RefSeq, Pfam, InterPro, Ensembl, ArrayExpress and data DOIs.

Back to top

Does Europe PMC search using synonyms?

Europe PMC will, by default, add known synonyms for your search term to expand your query. For example, a search for 'cat' will also include 'felis domestica'. You can turn synonyms off using the Advanced Search form.

Back to top

Europe PMC Search

How do I search Europe PMC?

The main Europe PMC site provides two search functions: a free text search, direct from the main search box, or an advanced search, from the advanced search page which provides you with a number of different parameter options.

You can refine your search by entering search syntax in the search box. The search syntax reference at the bottom of this page includes many examples.

Back to top

What am I searching on Europe PMC?

PubMed abstracts 25 million, full text 3.3 million, open access 1 million, other abstracts 5.4 million (including Agricola, Patents, Thesese, Chinese Biological)

The diagram above shows the approximate breakdown of Europe PMC content. The content scope of Europe PMC covers both abstracts and full text articles, with some full text articles being available as Open Access content that can be downloaded and re-used. Click here for more information on the Europe PMC Open Access subset. Links to content providers are given in the following list:

Code Definition Details of data source
AGR Agricola Agricola is a bibliographic database of citations to the agricultural literature created by the US National Agricultural Library and its co-operators. http://agricola.nal.usda.gov
CBA Chinese Biological Abstracts CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.
CTX CiteXplore Manual user-submitted records, added by the EBI.
ETH EthOs Theses PhD theses (British Library)
HIR NHS Evidence UK Clinical guidelines
MED PubMed/MEDLINE NLM PubMed: http://www.ncbi.nlm.nih.gov/pubmed NLM: the National Library of Medicine (NLM) is the world's largest biomedical library. It explores the uses of computer and communication technologies to improve the organization and use of biomedical information. http://www.nlm.nih.gov/ MEDLINE: the National Library of Medicine's database of bibliographic citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences. http://www.nlm.nih.gov/pubs/factsheets/medline.html
NBK Europe PMC Book metadata This source type denotes full text books on the Europe PMC Bookshelf that are not initially provided with a PMID 'MED' source metadata record.
Where a full text book is received from the NCBI without a corresponding PMID 'MED' type metadata record, an 'NBK' metadata record will be created with the same 'NBK' number as the book. The metadata will be replaced by a PMID 'MED' type record if later made available. The full text book always retains its 'NBK' number.
PAT Biological Patents http://www.epo.org/
PMC PubMed Central PMC is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). http://www.ncbi.nlm.nih.gov/pmc/

See also: Europe PMC 'About' page for related information.

Back to top

Does my search cover the full text?

Yes, all keyword searches, by default, query the full-text of over 4 million Europe PMC articles.

See also: How are my Search Results Displayed?

Back to top

How do I search by journal title?

You can search for certain journals directly from the free text search box by vernacular title, instead of needing to type out the name in full. Europe PMC currently handles six commonly used acronyms and abbreviations:

  1. EMBOJ for The EMBO journal.
  2. JAMA for Journal of the American Medical Association.
  3. JBC for The Journal of Biological Chemistry.
  4. NEJM for The New England Journal of Medicine.
  5. PNAS for Proceedings of the National Academy of Sciences of the United States of America.
  6. NAR for Nucleic Acids Research.

Europe PMC will consider adding other vernacular titles to the list by request.

You can search for journal titles directly from the advanced search page by typing into the journal field – the autocomplete function will suggest likely matches that you can choose from.

When searching for a journal using its full name from the free text quick search box, the 'JOURNAL' search term syntax can be used, for example: JOURNAL:"Advances in Pharmacological Sciences" to make the search more accurate.

You can access the Journal List from 'Tools' in the navigation bar. The list features titles that deposit content to Europe PMC and can also be used as a quick way of browsing the contents of a particular journal. For bibliographic information about a Europe PMC journal, click on the ISSN alongside the title in the Journal List.

You may also search for specific journal titles using the appropriate field search terms, for example by ISSN number: ISSN:1687-6334.

See also: How do I make the most of my search? and also section 2.1 for search syntax.

Back to top

How are my search results displayed?

When you carry out a search in Europe PMC, all the citations found are presented as shown on the screenshot below:

Search results page

The number of search results is shown at the top of the list, along with 'Sort by' options, which default to relevance. See also What happens when I sort by relevance?

If the full text is available the phrase 'Free full text article' is presented as a hyperlink underneath the article title. Refine the search results by selecting any of the authors listed, or the journal name.

The search results can also be filtered using the 'Content types' on the right-hand-side of the screen.

Back to top

How do I search by author or ORCID?

You can use the author search field on the advanced search page, which will offer you likely matches as you type, if an author has an ORCID the auto-suggest will also display it as shown below:

Author name search demonstrating an author and ORCID suggestion

Note that list of names presented is ordered by the number of articles an author has published. Alternatively you can just enter an ORCID into the author field, and the author will be found if he/she has an article contained in Europe PMC. For example:

Author ORCID search

If you wish to search only for an author who is part of a consortium you can select the 'Investigator' field from the 'All bibliographic fields' list, example given in the screenshot below:

Using Bibliographic Fields to search for Investigator

See also: How do I make the most of my search?, 'How do I link my articles to my ORCID?, and How are ORCIDs used in Europe PMC?

An ORCID can also be typed directly into the quick search box, as opposed to using an author's name:

Searching by ORCID

In the quick search box you also have the option to search for authors in the following formats:

Authors are not listed by initial and last name in Europe PMC (i.e. 'J Smith'), so this format is not supported.

The author search (via the free text search box) works by first matching the entered name to a list of known authors; algorithms are used in the matching process, which then generates an 'AUTH' syntax-type search.

The above searches also include authors that are part of a consortium. In the example below the author is listed in a separate 'collaborators' block in the citation details page, for example:

Collaborating authors section

Should you wish to only search through the list of collaborators the following syntax can be used in the quick search box (or selected in the advanced search form as described above):

INVESTIGATOR:"John Smith"

Back to top

How do I make the most of my search?

There are many ways to search for articles in Europe PMC. The most obvious being a free-text search at the top of the screen. Europe PMC content can be retrieved using all the metadata that is indexed, as well as the article text itself. The scenarios discussed below include advanced search functionality, free text searching, and the use of specific search syntax.

Scenario: Using the Advanced Search Form

The Advanced Search provides a number of optional parameters, which assist you to create precise search queries without the need to remember search syntax.

As a query is built, a 'query builder' box at the top of the form displays the search syntax used by Europe PMC. This syntax can be edited and copied. The query syntax can be pasted into the main Europe PMC search box. The journal name, author, funder and grant ID fields provide auto-suggest functionality in a drop-down menu to help you complete the fields. The journal name suggestions (as shown below) are ordered by the number of articles published.

Journal suggestions

Many of the search fields support the selection of multiple values by using the grey '+'' button beside the field. These can be combined together with AND, OR and NOT operators.

Add fields using the advanced search form

Scenario: Article Title and Author Searching

Users have the choice of either using the Advanced Search form to facilitate searching, or to manually enter search terms in the quick search box. One of the simplest scenarios is searching by article title using the quick search box on the home page, for example by entering an article title/part title as follows:
Leukotriene E4

You could further refine the search by using the term 'TITLE', for example:
TITLE:"Leukotriene E4 Th2"

However if an exact title is known, and it is fairly unique, it is usually sufficient to use a full title:
"Leukotriene E4 activates human Th2 cells for exaggerated proinflammatory cytokine production in response to prostaglandin D2"

It is recommended that the title be placed within speech marks to find exact matches.

You can combine search terms to find an article, for example using part of the title and the author:
Leukotriene E4 "Pettipher R"

See also: How do I search by author or ORCID?

Scenario: The Use of Other Article Information

It's possible to search for articles by a wide variety of article information. Search syntax can help you to search accurately, and these are all listed in the search syntax reference together with hyperlinked examples. For example, if you wanted to find an article published in 2004, related to mouse research and knew one author was XJ Chen, a search using the 'TITLE' and 'PUB_YEAR' search terms is possible:
TITLE:"mouse" AND "Chen XJ" AND PUB_YEAR:2004

Other combinations of search terms are also possible to assist in locating research.

Scenario: Using Boolean Operators

Use the Advanced Search form to facilitate searching, or to manually enter search terms in the quick search box. A Boolean operator is a logical connection; a word that is used to connect two or more search terms. You can use the AND, OR and NOT operators to control search results, for example:

Search Description
vitamin d receptors (elderly NOT children) Vitamin d receptors where elderly is mentioned, and children are not mentioned
husbandry (cats AND dogs) Husbandry where both cats and dogs are mentioned
husbandry (cats OR dogs) Husbandry where either cats or dogs are mentioned
husbandry (cats NOT dogs) Husbandry where cats are mentioned, but not dogs
TITLE:"mouse" AND AUTH:"Chen XJ" AND PUB_YEAR:2004 Articles where the word mouse is in the title and one of the authors is 'XJ Chen', and the article was published in 2004.
TITLE:"mouse" NOT PUB_YEAR:2004 Articles where the word mouse is in the title and the article was not published in 2004.

Scenario: Wildcard Operator

The wildcard asterisk character (*) can be used to facilitate searching. For example when searching for any article that has any accession number type:
ACCESSION_TYPE:[a* TO z*]

You can also use this operator to search for any word that starts with a base word, for example to search for any word that starts with "neuron":
neuron*

This will search for neuron, neurone, neuronal etc.

Scenario: Data Links and Data Citations

The Advanced Search form provides the user with a very convenient facility to find data links and citations. Data citations are papers that cite a selection of database records, as mined from the full text. Data links are also provided by third party databases to Europe PMC articles. The databases included are listed in sections 2.7 and 2.8 of the Search Syntax Reference. The screenshot below shows the relevant section on the Advanced Search form.

Options in data links menu

You can also select any combination of links and citations using the Boolean operators available on the form.

Back to top

How do I limit my search by content type?

All searches can be restricted by content type. For example the 'Content types' filter on the right side of the screen as shown in the example below:

Example of Content types sidebar

The sidebar also gives a count (in brackets) of the number of results in each content type. Clicking or tapping on a content type updates the results list accordingly.

Alternatively you can use the 'Filters' section of the Advanced Search form to restrict your results to a particular content type.

Back to top

How do I search by PMID or PMCID number?

Simply enter the PMID (PubMed ID) number into the search box and this will usually find a result. However the PMID can more precisely be specified with the search syntax 'EXT_ID:'. PMCIDs (PubMed Central IDs) always require the prefix PMCID, for example:
PMCID:PMC3013671

Note that PMIDs are unique when used in conjunction with a data source. When searching for a PMID that yields more than one result, the data source can be specified to find the exact match, for example the following search yields three results
EXT_ID:526631

Specifying the data source using the 'SRC:' search term, along with the PMID will find a unique result, for example:
EXT_ID:526631 AND SRC:MED

The permissible values for the 'SRC' search term are given in the 'Code' column of the table found under: What am I searching on Europe PMC?

Back to top

How do I search by grant number/agency?

Using the advanced search form you can easily search for articles associated with specific funders or individual grants using the funder or grant id fields – both of which are auto-suggest fields, under Funding Attribution:

Screenshot of advanced search page Funding Attribution section

You can alternatively use the free text search box and use search syntax (see Search Syntax Reference). For articles related to a specific grant, you should use 'GRANT_ID:' followed by the number which you are interested in, for example:
GRANT_AGENCY:"Wellcome Trust" GRANT_ID:"069683"

Alternatively, you can use the grant finder tool; to find grants from Europe PMC funders.

Back to top

Can I search using MeSH terms?

Note: MeSH (Medical Subject Heading) terms only apply to most PubMed records, not Europe PMC full text. An option is provided on the advanced search form that will include/exclude MeSH terms from a search as shown below:

Filters section, option "Synonym query expansion"

Alternatively you can search for Medical Subject Headings (MeSH) terms using the keyword search term in the quick search box, for example:
KW:"dogfish"

Back to top

How do I search only selected sections of an article?

The fastest way to search sections from all the Europe PMC full text articles is by using the Advanced Search form.

You can search the following sections of articles: Abbreviations, Acknowledgements & Funding, Appendix, Author Contribution, Case Study, Competing Interest, Conclusion, Discussion, Figures, Introduction and Background, Keywords, Materials and Methods, Others, References, Results, Supplementary Information and Tables.

In the 'Filters' section of the 'Advanced Search' form, select the 'Article Sections' drop down, where you can select one or more sections as required. The text-box to the right of the section allows for free-text input. In the example below the user has chosen to look for the term 'mRNA' in the 'Discussion' sections of articles, but only where the same term does not appear in the 'Introduction and Background' sections of articles.

Article Sections dropdown in Filters section of advanced search

You can also choose to search the required sections from the free text quick search box, using search terms. The search-term syntax can be found on the Search Syntax Reference, and it is also shown in the 'Query Builder' box on the Advanced Search form. When building a search as in the example above, the following search query is generated:
(DISCUSS:"mRNA" NOT INTRO:"mRNA")

To enable section searching Europe PMC full text content has been indexed at the section-level, where the sections can be identified. The ability to identify the sections depends on the structure of the articles provided, and this can vary. Depending on the section, the coverage from the open access subset of Europe PMC, for example, varies from 1% to 80%.

Back to top

Europe PMC Accounts

What can I do with a Europe PMC account?

With a Europe PMC account you can sign in to save search queries. Other features will be added in future.

Back to top

How do I sign in to Europe PMC?

You can sign into Europe PMC, to save your searches, with external services including ORCID, Twitter and Europe PMC Plus. Alternatively you can create a Europe PMC account.

  • Sign in with ORCID

    You will be taken to a page on the ORCID website where you can either enter your ORCID login details or create a new ORCID account. You will be redirected back to Europe PMC after signing in.

  • Sign in with Europe PMC

    You can sign in with a Europe PMC account. This is not the same as the Europe PMC Plus account which is used to submit manuscripts. You will need to register to create a new Europe PMC account. Find out about creating a Europe PMC account.

  • Sign in with Twitter

    You will be taken to a page on the Twitter website where (providing you are already logged into Twitter via your web browser) you simply authorise Europe PMC to use your Twitter account. You will be redirected back to Europe PMC after authorisation.

  • Sign in Europe PMC Plus

    You can now sign in with a Europe PMC Plus account. You will be taken to the Plus website and redirected back to Europe PMC after signing in.

Back to top

How do I create a Europe PMC account?

Click the 'create an account' link at the very top of the site header.

You will be taken to a form where you can enter your name, email address a password to create a new Europe PMC account.

After submitting the registration form you will receive an email with an account activation link. Once you have activated your account you will be able to access your first saved search query and save additional search queries.

Back to top

I have created a Europe PMC account but I can't access my saved searches

You may not have activated your Europe PMC account. Please check your email for the activation link.

You may have saved searches using another sign-in (eg. ORCID or Twitter). You can connect the accounts to merge your saved searches into one account.

Back to top

I don't need a Europe PMC account anymore. How do I delete the account?

You may access the delete account page by hovering on your display name on the top right corner > Manage account. You will be taken to the Connect account page. Delete account can be found on the left side navigation menu.

Back to top

Europe PMC Author Profiles

How do I get a Europe PMC author profile?

If you have an ORCID iD , then by default you will have a Europe PMC profile page. An ORCID iD is a unique identifier which distinguishes you from other researchers. All data displayed on Europe PMC author profiles is openly available from Europe PMC and ORCID.org. Any publications which you have linked to your ORCID iD (and are marked as visible to Public, or Everyone, or Trusted Parties) will be displayed on your Europe PMC profile page.

Back to top

Why are there no publications displayed on my author profile?

There are three possible reasons why publications are not displaying on your Europe PMC author profile:

  1. You have not linked any of your publications in Europe PMC to your ORCID iD. Use our simple tool to link your articles to your ORCID iD.
  2. It is less than 24 hours since you linked your publications to your ORCID iD (there can be a delay of up to 24 hours before Europe PMC is updated with any changes you make to your ORCID record)
  3. Your 'works' in your ORCID profile are marked as only being visible to you. You will need to update your ORCID privacy settings .

Back to top

How do I prevent publications from being displayed on my author profile?

Modify your privacy settings on the ORCID website. Any publications marked as Private or Only Me will not be displayed on your Europe PMC profile.

Back to top

How do I download the chart on my profile page?

You can download an image of the chart (in PNG, JPEG, PDF or SVG format) to include in your CV or website by using the Download chart button.

Back to top

How do I access an author's profile?

All author profiles on Europe PMC are public. There are various ways access an author's profile including:

  • Link to an author's profile from an abstract page, under the section 'ORCIDs linked to this article'.
  • Search for the author by name in the Advanced Search - if they have an ORCID iD which has been linked to Europe PMC it will be displayed in the suggestions.
  • Enter the author's ORCID iD in the main search box.

Back to top

What are open citations?

On Europe PMC author profile pages, open citations are based on the reference sections of articles which are available through open data sets. This includes full text articles in Europe PMC and citation services such as CrossRef. Find out more about Europe PMC's citation network.

Back to top

What can I do with my search results?

How can I get the full text article?

Full text articles can be accessed in two ways following a search on Europe PMC. If the full text is available for an article the phrase 'Free full text article' is presented as a hyperlink underneath the article title. This is highlighted in the red box in the screenshot below:

Red box around Free full text articlel ink

The Europe PMC search results list can also be filtered to show only results that have full text, or even only Open Access full text. The screenshot below highlights the filter options found on the right-hand side of the screen:

Content types sidebar

Back to top

How can I sort my results?

Europe PMC results can be sorted as follows:

  1. By relevance
  2. By date
  3. By times cited

The sort options appear above the search results list, shown highlighted in the red box below. The sort applied to the search results list is highlighted, and defaults to 'Relevance'.

The 'Times Cited' sort shows the most highly cited articles, listed in descending order. The counts per paper in Europe PMC might be somewhat lower than the counts achieved in Scopus or Web of Science because we do not have access to the same content as these resources. However, highly cited articles in Europe PMC correlate with highly cited papers on other platforms, and the information on where papers are being cited is freely available.

For more information about how Europe PMC derives its citation counts, see How does Europe PMC derive its citations network?

Back to top

How do I set up an RSS feed?

You can either subscribe to a pre-defined RSS feed, or customise one to suit your needs. Europe PMC has a list of pre-defined feeds, available via the following link. The list of pre-defined feeds includes an option to view the latest articles added to Europe PMC or follow new publications from each of the Europe PMC funders.

Pre-defined RSS feeds

  • Europe PMC Blog
  • Top 10 viewed articles on Europe PMC (last 7 days)
  • Latest articles added to Europe PMC (last 7 days)
  • Latest journal titles added to Europe PMC (last 60 days)

User-defined RSS feed

You can set up a user-defined RSS feed based on any Europe PMC search: using free text, or any search field. To set this up you would do the following:

  1. Run a search of interest, for example using a medical subject heading e.g. KW:Dogfish.
  2. Use the RSS feed icon shown at the top of the results list to select the feed, and then add to your browser as required.

Note that some browsers require an extension to be installed to support RSS feeds.

Back to top

How can I export citations from my search results?

Article metadata can be downloaded in several different formats. Full text is also available but only for articles in the open access subset.

The export option can be found near the top-right of most pages. It can be used in the following ways:

  • To export the results of a search, follow the Export link on any search results page, then select your desired format. Follow the 'Next' link, then 'Start Download'.
  • A new window will open while the download is in progress. You can download up to 50,000 citations, but please be aware that there will be a delay while the file to be created and transferred to your computer.
  • To export a selection of records from a search, select the checkbox at the top of the page to select the 25 results on the page, or select the checkbox to the left of each title you wish to download. You can run multiple searches, choosing different records from each, and the system will remember your selections, as long as you do not leave your session inactive for one hour. Then follow the 'Export' link on the search results page, select your desired format, and follow 'Next', then 'Start Download'.
  • To export a single record, go to its abstract or full text page. Follow the 'Export' link, select your desired format, and then follow 'Next', then 'Start Download'.

Please refer to the documentation of your local system and installed applications for information on how to open the files once downloaded.

Back to top

Which Europe PMC export format can I use with Excel, and how do I use it?

Microsoft Excel is capable of importing a number of different file formats. Many users are familiar with the CSV (Comma Separated Values) format. This is a generic format that most spreadsheet applications can import. To export a CSV file, choose the option 'CSV (comma separated - Excel)' from the Export menu.

We also offer a tab separated format 'TSV (tab separated - Excel)'. This export format file will have a TSV (Tab Separated Values) file extension.

Back to top

How can I email citations from Europe PMC to myself or others?

Follow the instructions for exporting search results above, but select Email as the Destination in the export dialog box.

Back to top

How can I import citations into my reference management program?

Export citations from Europe PMC using the 'RIS' export format. The RIS file can be imported into many popular reference management applications, for example: EndNote, Reference Manager etc. See instructions on exporting search results above. The screenshot below shows the 'RIS' export option highlighted:

Back to top

How do I track data citations?

You can search for papers that cite a selection of database records. Citations are available for a number of different databases: European Nucleotide Archive, UniProt, PDB, OMIM, RefSNP, RefSeq, Pfam, InterPro, Ensembl, ArrayExpress. You can also find papers that cite data DOIs. These searches can also be used in either the SOAP or RESTful Web Services.

You may wish to setup an RSS Feed alert when citations are made for a particular database. To do this, run the search of interest, for example: ACCESSION_TYPE:omim, then use the green RSS Feed icon above the search results to setup the alert.

You can also find articles that have not yet been linked to the database of interest (where references have been found in the full text, but they have not been provided as cross-references to Europe PMC). For example use: ACCESSION_TYPE:sprot AND HAS_UNIPROT:N.

Back to top

How do I find other/related citations?

From the abstract/full text view of an article, you can use the Citations tab to access articles cited in the original article, as well as find articles which cite the original article. Here you will also find a link out to the citation index in the Web of Science record.

The Related Articles tab also allows you to access citations considered to be closely related to the original article. Citations can be selected for export by selecting the checkbox on the left of the title, this is also described in the section on exporting your search results.

Back to top

How do I use the BioEntities tab?

When database records are submitted or curated, references to the literature are frequently added, and made available via the 'BioEntites' tab (see screenshot below). These article citations from the databases are exploited in Europe PMC - you can click the links to move from the article back to the original database record. For example below, you can see that there are 65 different UniProt records that cite this one article. Other databases that provide cross-links in this way include ENA, InterPro, PDB, IntAct, ChEMBL, ChEBI and ArrayExpress.

As well as database cross-references, we also apply text mining to the full text articles and abstracts. Several types of terms are text-mined, including gene symbols, diseases, chemicals, organisms, Gene Ontology terms, and accession numbers. Accession numbers are a special case as they represent specific data citations, in a similar vein to article citations within an article. In the above example, there are 16 gene symbols mined out of the full text (which are linked back to UniProt).

Text-mined terms can be browsed under the BioEntities tab for full text articles. For abstracts, terms of interest can be highlighted (as shown below). In both cases, terms link to related data resources – with the exception of 'Disease' bioentities, where the link initiates a new search on Europe PMC for that term. On the Bioentities tab, the magnifying glass adjacent to each term, will initiate a new search on Europe PMC for that term.

Protein Data Bank, and some chemical structures, can be viewed via the bioentities tab. Where this is the case a 'View Structure' link will appear next to the citation.

See also: How are links on the BioEntities tab derived?

Back to top

With Europe PMC you can quickly and easily find relevant additional content via externally provided links. Where these exist for an article or abstract they can be found using the 'External Links' tab as shown below:

External Links tab

With the Advanced Search form you can more precisely find any of the links by specifying the provider of interest. Use the drop-down at the bottom of the form as shown below:

External links dropdown on advanced search page

Back to top

Europe PMC Content

What is the difference between an abstract and full text article?

In Europe PMC terms - an abstract is a brief summary of a research article. You can view the abstract of an article in Europe PMC by following on a search result. If available, you can view the full text research article either by using the full text icon under a search result article title, or by following the full text link on the right side of the abstract page. Some full text is only available on external sites, and in some cases a subscription may be required. The article may be under a publisher's embargo; if so the date when the article full text is due to be released (the embargo date) will be shown on the abstract page.

Back to top

The article embargo date has passed, why can't I access the full text?

If the article is under a publisher's embargo, the embargo date is shown on the abstract page in Europe PMC. If the full text of the article is released by the publisher on the specified embargo date, there may be a delay of up to 48 hours before it appears in Europe PMC. Sometimes the full text may be available in Europe PMC before the embargo date, if the publisher releases it in advance of the embargo date.

Back to top

How do I save my search?

On the search results page use the 'save search' link at the top of the page to save your search query.

You will need to sign in to save your search query. If you have not signed in before you have the option to sign in with external services including ORCID, Twitter, Europe PMC Plus or alternatively you can create a Europe PMC account using your email address. Find out how to create a Europe PMC account

Once you have signed in you will be asked to give your search query a memorable name.

Find out how to access your saved searches and edit your saved searches.

Back to top

How do I access my saved searches?

Your saved search queries can be accessed from the menu in the top-right corner of the Europe PMC website.

Back to top

How do I run my saved searches?

Go to your saved searches (which can be accessed from the menu in the top-right corner of the website), then re-run the search by clicking or tapping on the name of the search.

Back to top

How do I edit my saved searches?

Go to your saved searches, then use the edit icon as shown in the screenshot below.

Edit icon, which looks like a pencil

Edit your query in the text field provided. You can refer to the Search Syntax Reference to refine your query. When you edit a saved search query, the original saved search will be overwritten.

Back to top

How do I delete my saved searches?

Go to your saved searches, then use the delete icon as shown in the screenshot below.

Delete icon, which looks like a trash can

Back to top

How many searches can I save?

You can save up to 100 search queries.

I have saved searches on another sign-in. Can I merge my saved searches to one account?

You can now connect accounts to merge your saved searches to one account. You can find Connect accounts by hovering on your display name at the top header as shown below.

How to find the menu to connect accounts

Back to top

What journals are currently available in Europe PMC?

See the Europe PMC Journal List for a list of journals which deposit content in Europe PMC. Content from a wide range of other journals is included in Europe PMC. Use the journal auto-suggest field in the Advanced Search form to search for specific journal names.

Back to top

Does Europe PMC contain the full text for all of the journals that are in its archive?

No. Journals that deposit their articles in PMC whose content is mirrored in Europe PMC fall into one of three categories:

  1. For several hundred journals, we have the complete contents of each issue, starting with the first issue. For the older journals in this group, the back issues of a journal (generally, anything prior to the late 1990s) are available as digitized (scanned) copies of the original print journal.
  2. For a smaller group of journals, we have complete issues and volumes for recent years, but not for all the early years of the journal.
  3. For other journals, we do not contain any complete issues, just a selection of articles, e.g. those that the journal has published as open access articles.

In all three categories, we have a journal's final published version of the respective articles. In addition to the final versions of articles provided by publishers, Europe PMC contains author manuscripts of selected articles from several thousand other journals.

See also What journals are currently available in Europe PMC?, How do research publications get into Europe PMC?, What are author manuscripts?, How does the author manuscript in Europe PMC differ from the article published in the journal? and What am I searching on Europe PMC?

Back to top

Does Europe PMC contain all that PubMed and PMC contain?

Overall, Europe PMC contains more than both PubMed and PMC. In brief, Europe PMC contains all of the PubMed abstracts, the vast majority of PMC content, plus additional content including patents, NHS clinical guidelines and Agricola records (for a detailed breakdown of Europe PMC content see What am I searching on Europe PMC?).

Full text publisher-provided content in PMC is subject to PMC Participation Agreements. Since July 2006, when Europe PMC (then branded as UKPMC) became the first PMC International centre, all PMC Participation Agreements have included permission to make a participating journal's content available at Europe PMC. Of those whose Participation Agreement pre-dates this, most agreed to this wider distribution of content, however some did not which means that approximately 250,000 articles in PMC are not available from Europe PMC; the vast majority of these are back issue articles.

See also Does Europe PMC contain the full text for all of the journals that are in its archive?, How is Europe PMC related to PMC International? and How does Europe PMC differ from PubMed and PMC?

Back to top

Does Europe PMC include articles written in languages other than English?

Almost all the material in Europe PMC is in English. A few journals in Europe PMC publish material in more than one language. For instance, the Canadian Medical Association Journal has some articles in (both) French and English. In this case, only the English material appears in Europe PMC's primary presentation of an article – the html full-text display. However, the journal's PDF version of the article may contain material in French as well as English. Another example is the Canadian Family Physician journal, which contains some articles that are available only in French; in this case Europe PMC provides this in both the full-text display and the journal's PDF version.

On the advanced search page there is an option to filter your search by language. In this instance, the languages listed refer to the original language of the article. Abstracts are converted into English once submitted to PubMed.

We also enable Europe PMC funders to supply abstracts associated with grant records in other languages, in addition to the primary description that is in English.

Back to top

What are author manuscripts?

Europe PMC Funders' Group organisations mandate that published research, arising from the research grants they award, must be made available through Europe PMC. One way this can be achieved is for authors to submit to Europe PMC (via Europe PMC plus) the final, peer reviewed manuscripts of such articles once they have been accepted for publication (the author manuscript) in this case the article content is what has been accepted by the journal for publication but it appears without the journal's house style. Papers submitted to Europe PMC are made accessible through both Europe PMC and PMC.

Some funders, most notably Wellcome, would always prefer the final, published version of the article and have made additional funding available to cover the costs related to open access (OA) article processing charges. In such cases, the publisher - as part of the OA fee - will take responsibility for uploading the final, published version of the article into PMC/Europe PMC. However, where publishers do not offer an OA option, then authors are required to self-archive author manuscripts in Europe PMC.

For more information on the difference between author manuscripts and published manuscripts, see question: How does the author manuscript in Europe PMC differ from the article published in the journal?

Back to top

How does the author manuscript in Europe PMC differ from the article published in the journal?

Most articles on Europe PMC are provided by the publisher and appear as they would on the publisher site. A small proportion of articles enter Europe PMC as author manuscripts; in this case the article content is what has been accepted by the journal for publication but it appears without the journal's house style. In more detail:

Though specific procedures vary from journal to journal, the publication process outlined here is typical for most research articles.

When an author submits an article to a journal, it is reviewed by one or more independent peer reviewers and the journal's editors, who decide whether to accept it for publication. As part of this process, the author may be asked to revise the article to meet the journal's standards for acceptance. The final accepted manuscript submitted to Europe PMC (the author manuscript) is the version that the journal accepted for publication, including any revisions that the author made during the peer review process.

The published version of the article usually includes additional changes made by the journal's editorial staff after acceptance of the author's final manuscript. These edits may be limited to matters of style and format or they could include more substantive changes made with the concurrence of the author.

When Europe PMC displays the author manuscript version of an article, the source data preceding the article title includes a reference to the published article, as in the illustration below.

Manuscript citatione example

See also How do research publications get into Europe PMC? and What are author manuscripts?

Back to top

How are ORCIDs used in Europe PMC?

Following the development of the ORCID-based Article Claiming tool (also see How do I link my articles to my ORCID?); Europe PMC has now integrated ORCIDs iDs into its website, search systems, and web services. This is proving useful for authors who want to show their publications list unambiguously on the Europe PMC website, allowing them to show for each article citation counts, linked data sets, and full text availability in Europe PMC. Hundreds of thousands of Europe PMC articles have been linked to tens of thousands of ORCID iDs, a count that grows significantly with each update from the ORCID foundation.

ORCID iDs are now shown in two ways on articles (also refer to screenshot below):

  1. In the article author list, when an author has linked the article to their ORCID iD, there is an option to search by ORCID iD rather than author name.
  2. As a list of ORCID iDs at the end of an abstract.

See, for example, the article that describes the initial sequence of the human genome.

ORCID-based author searching is particularly useful for people who have frequently occurring last names, or have changed their name, but also in the case of Consortium authorship, it allows scientists to claim their contribution to these works - something that name-based author searching cannot do in many cases.

For those interested in programmatic access, we have incorporated ORCIDs into the core response of the RESTful web service, linking the ORCID to specific author names as far as possible, and including a complete ORCID list for each record.

If you use the Europe PMC Article Claiming tool and/or make your ORCID bibliography public, your ORCID will be shown in Europe PMC as described above, when there is corresponding content available. The associations made using the article-claiming tool become available in Europe PMC at least daily.

Back to top

How can a journal/book be added to Europe PMC?

This process is managed by the NCBI, Europe PMC being a recipient of the content deposited. A guide and FAQ is provided to explain the process of adding journals to publishers, and also to take them through an application. There is also guidance for publishers that would like to add books to the Europe PMC Bookshelf.

Back to top

Additional Services and Tools

How do I submit a manuscript?

Anyone funded by at least one of the Europe PMC Funders can submit an author manuscript (see also: What are author manuscripts?) for inclusion in Europe PMC. Each submission must be approved by the Principal Investigator (PI) although colleagues may submit documents on their behalf.

To submit a manuscript, access the Europe PMC plus service (see also: What is Europe PMC plus?) and login. Access the My Manuscripts tab, select 'Submit New Manuscript' and follow the instructions.

You will be required to:

  • Set up your manuscript – provide the journal & article title information and the supporting grant information.
  • Upload your documents – provide the final, peer-reviewed version of the manuscript (see also: What are author manuscripts?). Europe PMC plus can accept a wide variety of document formats and also allows for upload of supplementary material.
  • Approve the PDF receipt – review documents to ensure completeness.
  • Approve the web version – once the manuscript has been converted to the appropriate PMC-ready format you will be able to review, amend and approve this final version.

Detailed help guides supporting the submission process can be found on Europe PMC plus.

Back to top

What is a Book?

Quality assessed full text on core biomedical subjects. A snapshot of a single completed book, or book component such as a chapter, the scope of which can be:

  • Technical monographs
  • Government reports
  • Multivolume monograph series
  • Traditionally website-based content such as Gene Reviews
  • Reference and professional books
  • Conference proceedings
  • Encyclopaedias

The mark-up of Books is based on the Book Interchange Tag Suite (BITS), a book model based on the JATS article model. The structure of BITS is the same as that of a journal article in many respects, but in others it is very different.

Back to top

What does the Europe PMC Bookshelf contain?

The Europe PMC Bookshelf receives content that is in the public domain (e.g., reports from US government agencies such as Agency for Healthcare Research and Quality) or specified by participation agreements. Additionally Wellcome-funded content is included following the extension of their Open Access policy to Books.

Back to top

How do Books relate to PubMed?

Bookshelf contents have a corresponding metadata record. However PubMed does not have citations for certain types of Bookshelf material, such as Help Documentation, that are considered out of scope for PubMed. In all cases where a PubMed ID is not provided, a Europe PMC metadata record is created to allow a book to be made discoverable on the Europe PMC Bookshelf. Such a metadata record is replaced should a corresponding PubMed one become available. See also: What am I searching on Europe PMC? and How do I find Europe PMC Bookshelf Content?

Back to top

How do I find Europe PMC Bookshelf content?

Following any search made via the main quick search box, the content types on the right-hand side of the screen, can be used to filter the results for Europe PMC Bookshelf content. As shown in the screenshot below, selecting the 'Content types' category of 'Books and Documents' restricts the results list to only Bookshelf content. It is also possible to find Europe PMC Bookshelf content using search terms as described in the Search Syntax Reference of this page.

Note that an option is also available on the advanced search form. The user can choose to search for a 'Publication Type' of 'Book and Documents'. The scope of this search is greater than just that of the Europe PMC Bookshelf, it will also return search results that link to the NCBI Bookshelf.

Back to top

How is grant data collected?

Grant award data is currently sent to the Europe PMC Helpdesk where it is first loaded into GRIST (GRant Information SysTem), and then into Europe PMC plus. Grant data is publicly available (with the exception of email addresses) via the grant finder and the GRIST API. Funders currently use a standard Excel template or an XML file, to send data to the Helpdesk, which is then loaded into GRIST. This is due to be replaced by a self-service web page that will accept the data in various formats.

Grant-article associations are processed into Europe PMC in the following ways:

  1. Via Researchfish (some Europe PMC Funders enrolled)
  2. Direct from Funders and other institutions (e.g. OpenAIRE plus)
  3. Direct from Europe PMC plus where associations are manually made by PIs.

Back to top

Are there any restrictions on the use of the material in Europe PMC? Can I download a batch of articles from PMC for research or other purposes?

Although access to the material in Europe PMC is free, the use of the material is still subject to the copyright and/or related license terms of the respective authors or publishers. See the Europe PMC Copyright Notice for more information.

You may not use any kind of automated process to download articles in bulk from the main Europe PMC site. Europe PMC will block the access of any user who is found to be violating this policy. Batch downloading of content in Europe PMC is supported by various methods including an FTP site, the Europe PMC-OAI service, and RESTful and SOAP web services – the content available via each method is summarised here.

See also the Europe PMC Open Access Subset page for more information.

Back to top

The external links service is a mechanism for external providers to publish links from articles in Europe PMC to related information or tools. More information on the service can be found using the link on the top navigation bar (see Tools > External links service), or directly at external links service.

For users of Europe PMC, the external links service enhances our existing content (see also What am I searching on Europe PMC?), and provides straightforward discovery and access to more resources. See also: How can I find external links?

Back to top

How do I participate in the Europe PMC external links service?

Please email us at labslink@europepmc.org, briefly describing the links you wish to share. We will assign you with the information you need to generate the files and upload your links.

Once you have generated files according to the instructions below, you will be able to upload data to a private directory on the external links service FTP site.

We have tried to make it easy, so that even if you do not have strong technical skills then it should be possible to contribute, and have developed some tools to help with file generation that are described on the Europe PMC external links page.

Back to top

What is Europe PMC plus?

Europe PMC plus provides manuscript submission and grant reporting services for researchers who are funded by Europe PMC funding organisations. Researchers can access citation counts for their articles, and a count of article downloads from the Europe PMC website as part of an Impact Report.

Europe PMC plus is accessed using the link on the top navigation bar, or directly at Europe PMC plus.

A username and password is required to access the service. These login details are provided to authors automatically via email, once their grant has been awarded. Authors who have forgotten or wish to reset their password can do this from the Europe PMC plus login page. Those submitting manuscripts on behalf of authors should create their own accounts.

The Europe PMC plus help page provides step-by-step user guides for manuscript submission, linking papers to grants and grant reporting.

Europe PMC plus also enables the Europe PMC funders to generate various types of grant reports, and monitor the papers their organisation's grantees have deposited.

Back to top

What is Europe PMC labs?

Europe PMC labs showcases prototype developments based on the content of Europe PMC. The developments are designed to enable deep searching of the literature and contextual linking to public databases in the life science domain. The goal is to expose these prototype developments to the users of Europe PMC, to seek feedback that could inform future development of Europe PMC services.

Europe PMC labs is accessed directly at Europe PMC labs.

Back to top

What is the grant finder?

The grant finder is a searchable database of the grants awarded by the 28 Europe PMC funders. Grant information can be searched by keywords in the project title or abstract, the Principal Investigator (PI) name, institution name, funder(s) name and grant ID.

The grant finder is accessed from the top navigation bar, by navigating to Tools > Grant finder, as shown in the screenshot below:

Back to top

How can I find out more about the science-writing competition, Access to Understanding?

Access to Understanding was launched towards the end of 2012 to encourage researchers to translate the findings of research articles into plain English. Please note that this competition has not been run from 2016 onwards.

Due to highly technical or domain-specific terms, much of the current scientific research is challenging for a non-specialist audience to understand. Access to Understanding sought to bridge this accessibility gap and make freely available research accessible to anyone interested in it. Each of the articles included in the competition were selected by a Europe PMC funder and are freely available from Europe PMC. You can read successful entries to the competition from previous years here.

Back to top

How do I link my articles to my ORCID?

Europe PMC offers researchers the ability to link articles to their ORCID (a unique researcher ID). The tool can be found under Tools > Orcid article claiming on Europe PMC.

Linking articles to your ORCID is a simple two-step process:

  1. Select your publications. After you have signed in via ORCID, Europe PMC presents you with a list of articles using the names and initials in your ORCID profile (from articles within Europe PMC). Select the publications that you wish to link using the check-box next to the article title.
  2. Review your bibliography and send to ORCID. Check the articles that you have selected and update your ORCID profile with the articles by using the 'send to ORCID' button.

See also: How are ORCIDs used in Europe PMC?

Back to top

Using SciLite annotations in Europe PMC

SciLite annotations in Europe PMC are text mined, biological entities which can be highlighted in the text of articles. For more information on using Annotations, visit our SciLite annotations page.

I have found an incorrect annotation. How can I report it?

If you find an incorrect annotation, or the annotation is too generic and is highlighted too often, you can report it by clicking or tapping on the highlighted term and using the 'Feedback' link in the popup window. Providing feedback helps us to remove problematic annotations and improve the overall quality and accuracy of annotations. You can also endorse annotations using the Feedback link, if they are useful to you.

Why do SciLite annotations not appear on every full-text article in Europe PMC?

We are only able to show annotations on articles with a CC-BY, CC-BY-NC or CC0 license. Currently this represents about 1,070,000 articles.

How are SciLite annotations sourced?

SciLite annotations on Europe PMC articles are generated using automated, text mining processes. Currently annotations come from 3 sources. You can find out more about where annotations are sourced from, and how to get involved if you are a text mining group, on the SciLite annotations page.

General Information

What are the benefits of Europe PMC?

Europe PMC enhances the visibility of research findings. Europe PMC content is freely available and can be accessed by all researchers, not just those based at an institution that subscribes to a particular journal.

Read more about the benefits in About Europe PMC

Back to top

How does Europe PMC differ from PubMed and PMC?

Europe PMC was developed in collaboration with the founders of PubMed and PMC, which are based in the United States. The principles of these services are similar - to provide free access to published peer-reviewed biomedical and health research abstracts and full-text articles (PubMed and PMC respectively) - but there are some distinct differences.

Unlike PMC, Europe PMC provides a single point of access to not only full-text articles but additionally the abstracts available through PubMed. The Europe PMC interface also offers novel features and functionality (for example ORCID), including links to other relevant content, integrated text and data mining tools and grant reporting services through Europe PMC plus (See also What are the benefits of Europe PMC?, What is Europe PMC plus?, and What is Europe PMC labs?). New developments are routinely explained on the Europe PMC blog.

If you would like to provide feedback on any aspect of Europe PMC, request a new feature, or participate in a user research session, please use our feedback form to get in touch.

See also Does Europe PMC contain all that PubMed and PMC contain?

Back to top

How is Europe PMC related to PMC International?

PMC International (PMCI) is a collaborative effort between the US-based National Library of Medicine (NLM), the publishers whose journal content makes up the PMC archive, and organizations around the world that share NLM's interest in archiving life sciences literature.

Europe PMC (formerly UKPMC) was the first PMCI centre and became operational in January 2007. PMC Canada was launched in October 2009. Both repositories receive their journal content directly from the US PMC archive. In all cases, manuscripts submitted locally via the author manuscript submission system have their content mirrored into the PMC network via PMC.

Essentially, the long term goal is to create a network of digital archives that can share all of their respective locally deposited content with others in the network. There are three primary reasons for doing this:

  • The probability of an archive surviving over the long term is greater if there are working copies of the archive in regular use at multiple sites around the world.
  • A producer or funder of research literature often will be more inclined to make the primary deposit of its material to a locally or regionally affiliated archive, rather than to one operated elsewhere in the world – there is more about the Europe PMC funders here.
  • Each site can integrate the journal articles in the archive with related material, such as national or regional practice guidelines, that has particular significance to its users.

Having a number of instances of the PMC database is based on the successful model adopted for genomic data. The International Nucleotide Sequence Database Collaboration comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three databases exchange data on a daily basis, but all three interfaces offer different functionality that benefits the molecular biology community.

See also How does Europe PMC differ from PubMed and PubMed Central?

Back to top

How can funding organisations join Europe PMC?

There are opportunities for European-based life sciences or biomedical research funders to join Europe PMC. See more on Joining Europe PMC.

Back to top

How do research publications get into Europe PMC?

Europe PMC Funders' Group organisations mandate that published research, arising from the research grants they award, must be made available through Europe PMC, typically within six months of being published. Authors can comply with funder mandates by making their research papers available through Europe PMC in two ways:

  • Method 1: by choosing to publish in a journal that will make the paper available through Europe PMC, immediately or within 6 months of publication.
  • Method 2: by self-archiving the final peer-reviewed author manuscript in Europe PMC. Papers deposited via this route can be embargoed for up to 6 months.

These methods vary in the version of the paper submitted, and the actions undertaken by the author and publisher. For more information on the difference between author manuscripts and published manuscripts, see question: How does the author manuscript in Europe PMC differ from the article published in the journal? The Wellcome has produced a useful Authors FAQ and Publishers FAQ in which further information can be found.

See also What are author manuscripts?

Back to top

Why does Europe PMC require the full text of every article in XML? Why do you not accept a PDF or html file?

Like PMC, we believe that XML currently is the most effective archival format for the textual portion of a journal article. It is essentially software- and hardware-independent, and therefore adapts easily to changes in technology. XML lets you preserve the structure and meaning of an article in a relatively simple and human readable form.

With a well-documented DTD (Document Type Definition), which serves as the "code book" for a piece of XML, you have something that people will still be able to decipher and use several generations from now, regardless of what technology is available then. This characteristic lends XML to being converted to a more advanced text recording format in the future. XML tagging also makes it easier for a computer to automatically 'read' the content of an article, which can help with more focused searching and with linking the article to related content in other databases.

The Europe PMC/PMC archive is based on the NLM Journal DTD, which was created specifically for archiving digital journal content.

Where an author self-archives the final peer-reviewed author manuscript in Europe PMC, they can do so in several file formats (see Europe PMC plus Help); the article will then be converted to XML and will undergo a rigorous quality control process after which the author will be asked to approve the final article before it is made available on Europe PMC.

Back to top

Europe PMC Quick Tour

To find out what Europe PMC is and how to use it, try our Europe PMC Quick Tour .

Back to top

Search Syntax Reference

This site offers an advanced search function as well the quick search function direct from the search box. Below is a table that describes basic syntax form and examples of how these can be used.

1. Direct search

Search syntax Result
J.Inorg. Biochem. 101:74-79(2007) Quick search in common notation style, with journal + volume + pageInfo + pub year
microtubule glycosylated Finds citations containing microtubule AND glycosylated (default behaviour)
microtubule OR glycosylated Finds citations containing microtubule OR glycosylated. Note that "OR" is case sensitive.
(fish OR bird) AND disease Finds citations containing either fish OR bird AND on top of that disease.
microtub* disease Finds citations containing disease AND terms that start with microtub. Wildcard usage is limited and not allowed when resulting in too many clauses.
microtubule cardiac -toxicity Finds citations containing microtubule AND cardiac but NOT toxicity
With quotes: "green grass" "green grass" with quotes) results in a search for green grass as a sequence of two words. Bear in mind that when you use 'stop words' (such as 'a','and','in','if' etcetera) within a quoted phrase search then this may give less accurate results due to the nature of the indexing mechanism.
Without quotes: green grass Using no quotes is always less strict, and will give back all citations where the words green and grass occur, not necessarily sequentially.

Back to top

2. Field search

Note: Advanced search uses field searches under the hood

2.1 Core bibliographic

Syntax word Description Example
EXT_ID: Search for a publication by external ID: i.e. the ID assigned to a publication at repository level. Together with the publication's source, they form a unique id of the publication. Click here for more details. EXT_ID:10826746
PMCID: Search for a publication by its PubMed Central ID, where applicable (i.e. available as full text) PMCID:PMC1287968
TITLE: Search for a term or terms in publication titles TITLE:aspirin, TITLE:"protein knowledgebase"
ABSTRACT: Search for a term or terms in publication abstracts ABSTRACT:malaria, ABSTRACT:"chicken pox"
PUB_YEAR: Search by year of publication in YYYY format; note syntax for range searching. PUB_YEAR:2000, PUB_YEAR:[2000 TO 2001]
E_PDATE: Electronic publication date, when an article was first published online. E_PDATE:2013-12-15, E_PDATE:20070930, E_PDATE:[2000-12-18 TO 2014-12-30], E_PDATE:[20040101 TO 20140101]
FIRST_PDATE: The date of first publication, whichever is first, electronic or print publication. Where a date is not fully available e.g. year only, an algorithm is applied to determine the value. FIRST_PDATE:1995-02-01, FIRST_PDATE:20000101, FIRST_PDATE:[2000-10-14 TO 2010-11-15], FIRST_PDATE:[20040101 TO 20140101]
P_PDATE: Print publication date of journal issue, when an article appeared in print format. P_PDATE:1982-10-01, P_PDATE:20140101, P_PDATE:[2000-12-18 TO 2014-12-30], P_PDATE:[20031114 TO 20141115]
EMBARGO_DATE: The date from which Europe PMC is permitted to provide access to the full text article. This date is held for articles received from March 2015. EMBARGO_DATE:[2015-03-01 TO 2015-03-31], EMBARGO_DATE:2015-03-15
EMBARGOED_MAN: Limit search results according to accessibility of the full text article regarding the EMBARGO_DATE. Assuming you request EMBARGOED_MAN:Y at the date 20160101 than this will be translated into EMBARGO_DATE:[20160101 TO *] and EMBARGOED_MAN:N to EMBARGO_DATE:[* TO 20160101]. EMBARGOED_MAN:Y, EMBARGOED_MAN:N
AUTH: Search for a surname and (optionally) initial(s) in publication author lists AUTH:einstein, AUTH:"einstein G"
INVESTIGATOR: Search for a publication by specifying an investigator INVESTIGATOR:"Orlandini F"
AUTHORID_TYPE: List publications that are associated with an ORCID AUTHORID_TYPE:ORCID
AUTHORID: List publications that are associated with a specified ORCID AUTHORID:"0000-0002-1767-9318"
AFF: Search for a term or terms in the author affiliation field AFF:ebi, AFF:"university of cambridge"
JOURNAL: Journal title – searchable either in full or abbreviated form JOURNAL:"biology letters", JOURNAL:"biol lett"
ISSN: Search for a journal by its ISSN; see the NCBI’s list of journals and ISSNs in PubMed ISSN:0028-0836
VOLUME: Search for journal volumes, most useful in combination with fields: JOURNAL/PUB_YEAR/VOLUME/ISSUE/SPAGE JOURNAL:"biology letters" VOLUME:10
ISSUE: Search for journal issues, most useful in combination with fields: JOURNAL/PUB_YEAR/VOLUME/ISSUE/SPAGE JOURNAL:"biology letters" VOLUME:10 ISSUE:2
SPAGE: Search for articles which begin on page N of their journal, best used in combination with JOURNAL or other fields SPAGE:25
LICENSE: Search for content according to the assigned Creative Commons license (where provided). The values assigned by publishers have been grouped as follows:
CC BY: "cc", "cc by", "cc-by"
CC BY-SA: "cc", "cc by sa", "cc-by sa", "cc by-sa", "cc-by-sa"
CC BY-ND: "cc", "cc by nd", "cc-by nd", "cc by-nd", "cc-by-nd"
CC BY-NC: "cc", "cc by nc", "cc-by nc", "cc by-nc", "cc-by-nc"
CC BY-NC-ND: "cc", "cc by nc nd", "cc-by nc nd", "cc by-nc nd", "cc by nc-nd", "cc-by-nc nd", "cc by-nc-nd", "cc-by nc-nd", "cc-by-nc-nd"
CC BY-NC-SA: "cc", "cc by nc sa", "cc-by nc sa", "cc by-nc sa", "cc by nc-sa", "cc-by-nc sa", "cc by-nc-sa", "cc-by nc-sa", "cc-by-nc-sa"
LICENSE:"cc by sa" OR LICENSE:"cc-by sa" OR LICENSE:"cc by-sa" OR LICENSE:"cc-by-sa"

returns the same count as:

LICENSE:"CC BY-SA"

All articles that have a Creative Commons license assigned can be found as follows: LICENSE:cc
EPMC_AUTH_MAN: Identify manuscripts that have been submitted via the Europe PMC plus (formerly UKPMC+) Manuscript Submission System EPMC_AUTH_MAN:y
NIH_AUTH_MAN: Identify manuscripts that have been submitted the NIH Manuscript Submission System NIH_AUTH_MAN:y
AUTH_MAN: Search for an article that has been submitted via a Manuscript Submission System AUTH_MAN:y
AUTH_MAN_ID: Find an article by specifying an manuscript submission ID AUTH_MAN_ID:EMS59581

Back to top

2.2 Article metadata

Syntax word Description Example
DISEASE: Search for mined diseases DISEASE:dysthymias
GENE_PROTEIN: Search for records that have GENE_PROTEINS mined GENE_PROTEIN:gng11
GOTERM: Search for records that have GOTERM mined GOTERM:apoptosis
IS_SCANNED: Search for scanned/OCR content IS_SCANNED:y
LANG: Limit your search to publications written in language X; see the Advanced Search page for a full list of languages LANG:fre, LANG:eng
GRANT_AGENCY: Limit your search by the funding agency which supported the research; see the Advanced Search page for a full list of grant agencies GRANT_AGENCY:"wellcome trust", GRANT_AGENCY:"medical research council"
GRANT_ID: Limit your search by ID of the grant which funded the research GRANT_ID:100229, GRANT_ID:71672
KW: Limit your search by keyword, including MeSH and other publisher-supplied terms KW:galactosylceramides, KW:"recombinant proteins"
CHEM: Limit your search by MeSH substance CHEM:propantheline, CHEM:"protein kinases"
HAS_ABSTRACT: Limit search results according to presence or absence of abstract HAS_ABSTRACT:y, HAS_ABSTRACT:n
ORGANISM: Search for mined organisms ORGANISM:terebratulide
PUB_TYPE: Limit your search by publication type; see the Advanced Search page for a full list of publication types PUB_TYPE:review, PUB_TYPE:"retraction of publication"

Back to top

2.3 Full text availability

Syntax word Description Example
BODY: Search for terms within the body of a fulltext article BODY:PCR
DOI: Search for publication by Digital Object Identifier (DOI) DOI:10.1007/bf00197367
HAS_DOI: Limit search results to those publications which do or do not have a DOI HAS_DOI:y, HAS_DOI:n
IN_PMC: Limit search results according to availability (or not) of fulltext article in PubMed Central IN_PMC:y
HAS_FT: Limit search results according to availability (or not) of fulltext article or book in Europe PMC HAS_FT:y
IN_EPMC: Limit search results according to availability (or not) of fulltext article in Europe PMC IN_EPMC:y
HAS_PDF: Limit search results according to availability (or not) of a PDF version of the fulltext article HAS_PDF:y

Back to top

2.4 Collection metadata

Syntax word Description Example
SRC: Search for articles from a particular repository; the available data sources are listed are listed in the 'code' column of the table under the question: What am I searching on Europe PMC? SRC:ctx, SRC:hir
HAS_XREFS: Limit search results to articles with cross-references to other databases; the available databases are listed in the Web Services Reference Guide HAS_XREFS:y
HAS_CRD: Limit search results according to presence or absence of links to related content. CRD is a database that provides comments about an article. HAS_CRD:y
HAS_TM: Limit search results to text-mined fulltext articles only (or not) HAS_TM:y
HAS_REFLIST: Limit search results to only those publications with a reference list (or not) HAS_REFLIST:y
CREATION_DATE: Search for publications by date of entry into the Europe PMC database, in YYYY-MM-DD format; note syntax for searching date range CREATION_DATE:2010-11-11, CREATION_DATE:[2010-11-11 TO 2010-12-11]
UPDATE_DATE: Search for publications by date of update in the Europe PMC database; note syntax for searching date range UPDATE_DATE:2011-11-11, UPDATE_DATE:[2011-11-11 TO 2011-12-11]
OPEN_ACCESS: Limit search results to articles that are Open Access OPEN_ACCESS:y
HAS_LABSLINKS: Lists articles that have links provided by 3rd parties (using the Europe PMC external links service) HAS_LABSLINKS:y
HAS_SUPPL: List articles that have supplemental data associated with them e.g. spreadsheets, video files, etc. HAS_SUPPL:y
LABS_PUBS: List articles that have external links by provider ID LABS_PUBS:1001

Back to top

2.5 Content type filter

Syntax word Description Example
SB: Limit search results to EuroFIR subsets SB:eurofir

Back to top

2.6 Books

Syntax word Description Example
ISBN: Search for book by ISBN where indexed ISBN:9780815340720
ED: Search for book by editor ED:jensen HAS_BOOK:y
PUBLISHER: Search for book by publisher PUBLISHER:"OUP Oxford" HAS_BOOK:y
HAS_BOOK: List the full text books on the Europe PMC Bookshelf HAS_BOOK:y
BOOK_ID: Find a full text book on the Europe PMC Bookshelf by specifying its 'NBK' number BOOK_ID:NBK27326

Back to top

2.7 Database cross references

Syntax word Description Example
ARXPR_PUBS: Show publications with links to given ArrayExpress ID ARXPR_PUBS:E-GEOD-22481
UNIPROT_PUBS: Show publications with links to given UniProt ID UNIPROT_PUBS:q1rfz4
EMBL_PUBS: Show publications with links to given EMBL ID EMBL_PUBS:KJ634683
PDB_PUBS: Show publications with links to given PDBe ID PDB_PUBS:2w3z
INTACT_PUBS: Show publications with links to given IntAct ID INTACT_PUBS:ebi-493556
INTERPRO_PUBS: Show publications with links to given InterPro ID INTERPRO_PUBS:ipr013998
CHEBITERM: Search for mined chemical names CHEBITERM:dihydrocapsaicin
CHEBI_PUBS: Show publications with links to given ChEBI ID CHEBI_PUBS:chebi:62806
CRD_LINKS: Show publications with links to given related content ID CRD_LINKS:22001008219
HAS_ARXPR: Limit search results to publications which are (or are not) cited by the ArrayExpress catalog and link to the relevant ArrayExpress record HAS_ARXPR:y
HAS_UNIPROT: Limit search results to publications which are (or are not) cited by the UniProt catalog and link to the relevant UniProt record HAS_UNIPROT:y
HAS_EMBL: Limit search results to publications which are (or are not) cited by the EMBL database and link to the relevant EMBL record HAS_EMBL:y
HAS_PDB: Limit search results to publications which are (or are not) cited by the PDBe database and link to the relevant PDBE record HAS_PDB:y
HAS_INTACT: Limit search results to publications which are (or are not) cited by the IntAct database and link to the relevant IntAct record HAS_INTACT:y
HAS_INTERPRO: Limit search results to publications which are (or are not) cited by the InterPro database and link to the relevant InterPro record HAS_INTERPRO:y
HAS_CHEBI: Limit search results to publications which are (or are not) cited by the ChEBI dictionary and link to the relevant ChEBI record HAS_CHEBI:y
HAS_CHEMBL: Limit search results to publications which are (or are not) cited by ChEMBL and link to the relevant ChEMBL record HAS_CHEMBL:y
HAS_OMIM: Limit search results to publications which are (or are not) cited by OMIM and link to the relevant OMIM record HAS_OMIM:y
CITES: Search for publications that cite a given article; article to be specified in the format, ID_src CITES:8521067_med, CITES:IND43783977_agr
CITED: Search for publications that have been cited N times CITED:100
REFFED_BY: Search for publications that cite the specified article; format, ID_source (the available data sources are listed in the Web Services Reference Guide) REFFED_BY:9497246_med

Back to top

2.8 Database Citations

Syntax word Description Example>
ACCESSION_ID: Find articles containing the specified accession number ACCESSION_ID:A12360
ACCESSION_TYPE: Find articles that cite ArrayExpress records ACCESSION_TYPE:arrayexpress
Find articles that cite BioProject records in the European Nucleotide Archive ACCESSION_TYPE:bioproject
Find articles that cite BioSamples records ACCESSION_TYPE:biosample
Find articles that cite data Document Object Identifiers ACCESSION_TYPE:doi
Find articles that cite European Genome-phenome Archive (EGA) records ACCESSION_TYPE:ega
Find articles that cite EM resources in the Electron Microscopy Data Bank (EMDB) ACCESSION_TYPE:emdb
Find articles that cite Ensembl records ACCESSION_TYPE:ensembl
Find articles that cite EudraCT records from the EU Clinical Trials Register ACCESSION_TYPE:eudract
Find articles that cite European Nucleotide Archive records ACCESSION_TYPE:gen
Find articles that cite Gene Ontology records ACCESSION_TYPE:go
Find articles that cite InterPro records ACCESSION_TYPE:interpro
Find articles that cite NCT clinical studies records from the US NIH ClinicalTrials.gov registry ACCESSION_TYPE:nct
Find articles that cite OMIM records ACCESSION_TYPE:omim
Find articles that cite Protein Data Bank in Europe (PDB) records ACCESSION_TYPE:pdb
Find articles that cite protein families (Pfam) records ACCESSION_TYPE:pfam
Find articles that cite ProteomeXchange records ACCESSION_TYPE:pxd
Find articles that cite Reference Sequence Database (RefSeq) records ACCESSION_TYPE:refseq
Find articles that cite records in the dbSNP Short Genetic Variations database (RefSNP) ACCESSION_TYPE:refsnp
Find articles that cite the resource of protein sequence and functional information (UniProt) ACCESSION_TYPE:sprot
Find articles that cite Treefam (database of animal gene trees) records ACCESSION_TYPE:treefam

Back to top

2.9 Section-level search

Syntax word Description Example
ABBR: Find articles with word "mRNA" in the Abbreviations section ABBR:mRNA
ACK_FUND: Find articles with word "ERC" in the Acknowledgements & Funding section ACK_FUND:ERC
APPENDIX: Find articles with word "ethics" in the Appendix section APPENDIX:ethics
AUTH_CON: Find articles with phrase "Smith" in the Author Contribution section AUTH_CON:"Smith"
CASE: Find articles with word "leukemia" in the Case Study section CASE:leukemia
COMP_INT: Find articles with phrase "no conflict" in the Competing Interest section COMP_INT:"no conflict"
CONCL: Find articles with word "osteoporosis" in the Conclusion section CONCL:osteoporosis
DISCUSS: Find articles with word "cardiovascular" in the Discussion section DISCUSS:cardiovascular
FIG: Find articles with phrase "in vitro" in the Figures section FIG:"in vitro"
INTRO: Find articles with phrase "protein interactions" in the Introduction & Background section INTRO:"protein interactions"
KEYWORD: Find articles with word "isoform" in the Keywords section KEYWORD:isoform
METHODS: Find articles with phrase "yeast two-hybrid" in the Materials & Methods section METHODS:"yeast two-hybrid"
OTHER: Find articles with phrase "transgenic mice" in the Others section OTHER:"transgenic mice"
REF: Find articles with word "COX2" in the References section REF:COX2
RESULTS: Find articles with phrase "in vivo" in the Results section RESULTS:"in vivo"
SUPPL: Find articles with word "supplementary" in the Supplementary Information section, indicating where supplementary data might be available SUPPL:supplementary
TABLE: Find articles with word "comparison" in the Tables section TABLE:comparison

Back to top

3. Search combinations

Combination Description
TITLE:pancreatitis IN_EPMC:y Finds citations in Europe PMC with word pancreatitis in title
AUTH:frossard TITLE:acute pancreatitis Finds citations from author Frossard with acute pancreatitis in the title
TITLE:panc* AUTH:frossard Finds citations from author Frossard where a word in the title starts with 'panc' i.e pancreatic, pancreas, PANCEA (A question mark represents a wildcard for one position, the star any number of positions)
JOURNAL:lancet AUTH:frossard Finds citations in journal The Lancet from author Frossard
ISSN:0140-6736 AUTH:frossard "acute pancreatitis" Finds citations from journal The Lancet (ISSN 0140-6736) with author Frossard and phrase "acute pancreatitis"
AUTH:frossard AUTH:steer HAS_ABSTRACT:y Finds abstracts by authors Steer and Frossard
GRANT_ID:058922 IN_EPMC:y Finds citations in Europe PMC with grant 058922 attached
GRANT_ID:"058992" AUTH:noor Finds citations containing author Noor with grant 058992 attached
GRANT_ID:05* AUTH:amin Finds citations containing author Amin and a grant starting 05 (A question mark represents a wildcard for one position, the star any number of positions)

Back to top