Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract GoPubMed is an Ontology/Knowledge-based literature search software product that searches PubMed for biomedical research articles. Your keywords are submitted to PubMed and the resulting abstracts are classified using Gene Ontology (GO) and Medical Subject Headings (MeSH).

MeSH is a hierarchical vocabulary covering biomedical and health- related topics. Gene Ontology (GO) is a hierarchical vocabulary for molecular biology covering cellular components, biological processes and molecular functions.

GoPubMed allows you to find information you need significantly faster through the use of biomedical background knowledge.

GoPubMed doesn't do the ranking, the user does!

GoPubMed retrieves PubMed abstracts for your search query and sorts relevant information into four (4) top level categories:

"What", "Who", "Where" and "When" -- which show the concepts, persons, institutions, places, journals and times which are relevant to your search query.

1) The “What” Category -- GoPubMed retrieves citations according to your query. The citations are linked in the "What" category. During the retrieval process GoPubMed fetches relevant abstracts from PubMed which contain biomedical concepts related to your query.

These biomedical concepts are grouped into "Top Categories". Papers are annotated with the "Top categories".

GoPubMed sorts abstracts according to the concept hierarchies of GO and MeSH which enable the combined search in molecular biology and medicine. The "What" categories help you to systematically explore your search results.

The ‘search results tree’ serves as ‘table of contents’, in order to structure the millions of articles in the PubMed/MEDLINE data base.

2) The “Who” Category -- This category helps you find leading scientists and centers in the biomedical field. After performing a search, authors of all relevant abstracts are listed under the "Who" category. By clicking on any author, his/her profile will be shown.

Advanced techniques for person disambiguation were used in order to categorize the more than 3 millions names, which appear in the PubMed database.

If two articles share the same author, GoPubMed evaluates their similar properties. The system thereby takes into account that the author of each paper often publishes about similar research topics, with the same co-authors and in the same journals.

The research topics are thereby connected to the concepts of the 'semantic network' in the background. The more concepts two articles have in common and the shorter the semantic distance in the network is, the more likely it is that the articles were written by the same person.

3) The “Where” Category -- Geographic localization of persons, centers, universities, etc, are found under the "Where" category. Moreover, the top journals for the query are also listed in this category.

"High impact factor journals" and "Reviews only" can be selected under this category. By clicking on the provided options the queries to find High impact factor journals and Reviews will be automatically generated.

4) The “When” Category -- The "Top years for query" section displays the "year" with the most publications next to it, based on your search query. The "Publication date" section contains today, last week, last month, last year, etc., which can be used to change the 'time window' of your search.

Advanced Semantic Search -- You can use the Ontologies to perform a 'semantic search' on millions of PubMed articles.

Advanced search capabilities are available in the "Where" category. Advanced Search makes it possible to filter publications by requiring certain terms or their child, journals, publications dates, etc. as part of the search results.

Advanced search can be used to refine the retrieval of documents, focusing on articles mentioning or excluding certain GO and MeSH terms, and selecting certain publications, authors, etc.

Hot Research Topics -- Hot Topics performs 'bibliometric analysis' to show you the growth of publications over time, the key concepts, authors, cities, countries and journals publishing on your topic of interest.

Literature growth over time - Hot Topics time lines show you:

a) The absolute count of papers over time for a term and its children.

b) The relative growth in comparison to the growth of the whole PubMed. Top authors, journals, cities, and countries - The top authors, journals, cities, and countries for papers related to a term have been determined based on the absolute publication count.

Co-author analysis - To understand the structure of author networks and to identify key players in a research area, Hot Topics shows you the co-authors via an author collaboration network.

World Map - GoPubMed provides a map of the world showing you the locations of research institutes working on your selected topic.

Ontology Editor -- Transinsight has created an "intelligent" taxonomy editor which uses available background knowledge to support the user during the process of ontology generation. The editor was especially designed for 'text mining' taxonomies.

While using the editor, the user does Not have to deal with complex software features, the interface is simple and intuitive.

System Requirements

Best viewed with Mozilla Firefox or IE8

For GoPubMed PRO

Database Server:

Application Server:


Manufacturer Web Site GoPubMed

Price Contact manufacturer.

G6G Abstract Number 20256

G6G Manufacturer Number 102754