Usability features

Autocompletion

By typing a minimum of three letters of your query, GoPubMed® automatically suggests the terms you could mean. You don’t even have to type as much as in the figure above. It’s enough to type only the first letters of the words, if the term consists of more than one word.
autocomplete

Clipboard

Add papers in your clipboard. Papers that are added to the clipboard are shown with clip-it.
The clipboard can be cleared using the option clearClipboard.

Show and hide the full abstract text

For a compressed view you can hide the abstract text.
show-abstracts show-snippets

Toggle between documents, statistics, top author, and clipboard view

If a query is performed, three options can be chosen: show the found documents, show the statistics for these documents, or show the top author for these documents (if less than 20,000 documents are found). If documents are in the clipboard, they can be shown by selecting clip-it. Removing documents from the clipboard is done by clicking clearClipboard.

Export

export allows exporting 100 abstracts to different formats.
export-menu

Login

In GoPubMed® you can create your own account and bookmark your favorite concepts and (if wanted) get informed about new developments. To login, click login and follow the instructions.

Under each document (abstract) we list a number of semantically related products. Semantically related means that we list only products that actually link to the content of the article.
related-products

Author profiles

Biomedical research happens in networks of researchers. GoPubMed® allows these networks to be searched for possible experts and collaboration partners, a feature that leads to tremendous timesaving when searching for appropriate experts. This feature is especially important in a specialized scientific world where it is becoming more and more vital to set up temporary teams of highly specialized experts. There is a lot of information on authors already present in the biomedical literature. GoPubMed® presents this information in the form of author profiles on top of the search result pages providing an overview of a specific author.

If an author profile needs corrections

In cases where you are not satisfied with the profile information we have automatically extracted, feel free to correct it. To assure the accuracy within the edited data, the GoPubMed® team will verify the information.
Editing a profile is simple:

  • You can edit the name, email, and affiliation information.
  • You can add papers to or remove papers from your profile by clicking the icon to the left of each abstract. If a paper is missing, you can run any additional searches to collect all papers for your profile.
  • The correction mode stays open until you save your changes or cancel editing.
  • The new profile information can take up to several hours to appear online.

Query Syntax

This section explains how GoPubMed analyzes queries and how they are evaluated.

To make it possible to search for annotated ontology terms we extended the original pubmed query syntax by special field IDs.
When the query is evaluated the analyzer algorithm checks which parts of the query can be evaluated locally on the server and which parts need to be sent to Pubmed to be evaluated. All parts containing field identifier from the original Pubmed syntax are sent to pubmed. On the basis of these results the so-called Advanced Search Algorithm expands and filters for the requested ontology terms.
Since we annotate and handle a couple of different ontologies beside GO and MeSH, we introduced further field identifiers to the original pubmed query syntax.

The following list summarizes our fields:

  • new Fields for annotated ontology concepts:
    • [go] Gene Ontology concepts
    • [mesh] MeSH concepts
    • Built-in Ontologies:
      • [geo] Cities and Countries of our Geo Ontology (used for affiliations)
      • [time] Publication date as ontology annotation
      • [author] Disambiguated authors
    • special control identifiers which are used to guide the result evaluation:
      • [uptodate] reannotate instantly after ontology has changed.
      • [onthefly] reannotate the articles of the current query.
      • [nocache] ignore the search result cache.
      • [maxdocs] setup the number of documents which are analyzed.
      • ALL Analyze all ˜ 20,000,000 articles of Pubmed.

Examples for valid semantic queries

Include concept and children in Title and/or Abstract

Syntax: concept[mesh] or concept[go]
All documents returned by this query contain the concept in Title or Abstract either exactly the name of the concept or their synonyms or one of its child concepts or their synonyms. If more than one [go] or [mesh] term are chosen, the returned documents will contain ALL these terms (or synonyms) or children (or synonyms).
Example:
France[mesh] AND Spain[mesh]

  • Returns i.e. PMID 19960840
    Title: Small parts: Crisóstomo Martínez (1638-1694), bone histology, and the visual making of body wholeness.
    Abstract: The Valencian engraver Crisóstomo Martínez (ca. 1638-1694) arrived in Paris in July 1687, commissioned to create an anatomical atlas. Impressed by Govard Bidloo’s Anatomia humani corporis (1685), Martínez decided to make a comparable work on osteology. …
    (MeSH assigned term: Spain)

    In this example Paris is a child of France, because Paris is a city.

Include concept and children in Affiliation

Syntax: concept[geo]
All documents returned by this query contain the concept in Affiliation either exactly
this concept name or one of its child concepts.
Example:
Germany[geo]
Returns i.e. PMID 20183784
Title: Neuroendocrine Tumors of the Small Bowels are on the Rise: Early Tumors and their Management
Affiliation: Klinik für Innere Medizin – Gastroenterologie und GI Onkologie, Vivantes Klinikum Am Urban, Berlin.
Returns i.e. PMID 20183773
Title: How Can we Provide Better Services for Demented Nursing Home Residents Suffering from Apathy?
Affiliation: Klinik für Psychiatrie und Psychotherapie, Charité Campus Mitte, Berlin.
Returns i.e. PMID 20175048
Title: Death in Seclusion – A Worldwide Phenomenon Illustrated on Fringe Groups in Munich.
Affiliation: Institut für Rechtsmedizin der Universität München, München.

Include concept and children in Publication Date

Syntax: concept[time]
All documents returned by this query i.e. 2010[time] are published in 2010
Example:

  • France[mesh] NOT 2002[time]
    returns all papers where in Title, Abstract or MeSH assigned terms the concept France appears and they were not published in 2002.
  • (France[mesh] OR Spain[mesh]) NOT 2002[time]
    returns all papers where in Title, Abstract or MeSH assigned terms the concepts France or Spain appear and they were not published in 2002.
  • (France[mesh] OR Spain[mesh]) -2002[time]
    returns the same result’s as in query b.
  • (France[mesh] OR Spain[mesh]) NOT (2002[time] OR 2003[time])
    returns all papers where in Title, Abstract or MeSH assigned terms the concepts France or Spain appear and they were not published in 2002 or 2003.
  • (France[mesh] OR Spain[mesh]) NOT (2002[time] OR 2003[time]) protein
    returns all papers where in Title, Abstract or MeSH assigned terms the concepts France or Spain appear, they were not published in 2002 or 2003 and the keyword protein appear in the any field of the paper (title or abstract or full text)
    Returns i.e. PMID: 19302717 (published in 2009)
    Title: Size-partitioning of an urban aerosol to identify particle determinants involved in the proinflammatory response induced in airway epithelial cells.
    Abstract: … RESULTS: Ambient aerosols were collected at an urban background site in Paris using four 13-stage low pressure cascade impactors running in parallel … In presence of a recombinant endotoxin neutralizing protein, the GM-CSF release induced by particles is reduced for all size-fractions

A complex semantic query

Example:

  • Proteins[mesh] (France[mesh] OR Spain[mesh]) NOT (2002[time] OR 2003[time])
    Returns all papers where in Title or Abstract either exactly this term (proteins or one of its synonyms i.e. Gene Proteins) or one of its child concepts (or their synonyms more than 18.000 protein names), the concepts France or Spain appear and they were not published in 2002 or 2003.