Contents

In a Nutshell - Searching is now sorted! How does it work?

GoPubMed allows significantly faster finding information needed through the use of biomedical background knowledge. GoPubMed doesn't rank, the user does! GoPubMed retrieves PubMed abstracts for your search query and sorts relevant information to the 4 top level categories:

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

GoPubMed is originaly based on this publication:

Andreas Doms and Michael Schroeder, "GoPubMed: Exploring PubMed with the GeneOntology ",
Nucleic Acid Research, 33 (Web Server Issue):W783--W786, 2005

The What Category

GoPubMed retrieves citations according with your query. The citations are linked in the "What"-category.

During the retrieval GoPubMed fetches relevant abstracts in PubMed which contain the biomedical concepts related for your query.

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

The concepts belong to the Gene Ontology ( GO), the Medical Subject Headings ( MeSH) and the Universal Protein Resource ( UniProt).


 

GO describes gene and gene products in different organisms. There are in GO three basic areas namely:

The MeSH hierarchy describes:


More specific headings are found at narrower levels.


By moving the cursor over a concept, you can see a brief description, its synonyms and its position in the tree.


Sorting abstracts according to the concept hierarchies of GO and MeSH enables the combined search in molecular biology and medicine. The "What"-categories help to systematically explore the results. The tree on the left serves as table of contents in order to structure the millions of articles of the PubMed/MEDLINE data base. By navigating the tree you can narrow down from thousands of search results to a few in seconds. Your benefits are tremendous time savings.

The Who Category

This category helps you to find leading scientists and centers in the biomedical area. After performing a search authors of all relevant abstracts are listed under the "Who"-category.

By moving the cursor on the authors name and clicking on "Profile", his/her profile will be shown. Novel and sophisticated techniques for person disambiguation were used in order to exactly categorize the more than 3 millions names, which appear in 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.

This approach leads to impressive accuracy. If at any point the system is not correct, it can be corrected by the users.

The Where Category

Geographic localization of persons, centres, universities, etc, are found under the "Where"-category. Moreover the top journals for the query are also listed in this category.

"High impact factors journals" and "Reviews only" can be selected here. By clicking on these options the queries to find High impact factors journals and Reviews will be automatically generated.

The When Category

The Years of the publications for your query are shown in the "When"-category. Using the section "Publication date" by clicking on today, last week, month, year, etc., the time window for the search can be changed.

The "When"-category is the citations time machine.

How to use GoPubMed?

Find It!

Searching by concepts, authors, journals, etc. is done using the same search strategies as in PubMed.

As examples of the more important search strategies can be mentioned:

  • To find concepts in Title and/or Abstract use [TIAB],
  • To find an author name use [AU]
  • To find an affiliation (University, Institute, Company, etc) use [AD].

After searching GoPubMed shows how many citations have been found for the query and the documents are displayed by GoPubMed.



"Show the statistics of the articles of your search result." shows graphically publications history, most active publishing authors, countries and cities for your query. The same information can be found in the What, Who, Where and When categories on the left. In these categories an ontological representation is given. We show you a helpful summary and point you to the most important information in the context of your question. Advanced statistics give you a comprehensive overview for your query.

It toggles between abstracts or snippets mode for all documents.

My Search

Previous Queries
Here you have instant access to your last queries.


Query
Here you can see the different parts of your query. By clicking on you can open the complete path to this term in the "What"-category.
Terms in a disjunctive combination, are marked with a as shown in the following figure.


Clipboard
Add papers in your clipboard. The papers which are added in the clipboard are shown with

The clipboard can be cleaned using the option

How to refine the search?

Refine features are shown in the tree to the left of the term . Simply click on it! "Require" and "Exclude" are filters to refine the search. They select all documents mentioning or excluding one concept and its children of a category.

Example: If you search for the MeSH term "Aspirin", it is marked as required in the tree. You can see, that GoPubMed has found over 40,000 papers. Have a look at the tree. There are over 26,000 documents related to "Named Groups" which you may not be interested in. Simply exclude this term from your search! See also the figures below.

Now all papers relating to "Named Groups" are filtered out by GoPubMed and almost 15,000 papers are left. That's still al lot to read, but you can exclude more terms and concepts you are not interested in and after a few more clicks there will be only a small number of papers in your search result.



Further search results

10 citations are shown in each page. Links to others pages using "go to page" are available at the bottom of the page.

Get all!

Simply searching for "All" annotates and shows all PubMed articles with GO and MeSH concepts, proteins, authors, affiliations, date and geo annotations. So you can get an overview about the frequency of specific terms amongst all theses papers or you can just pass the time reading.

WWWW: Narrowing your search result

When people search, they have questions in mind. Consider the following questions and see below how GoPubMed helps answering them. Few clicks bring you from some general keywords to an answer. See important concepts at a glance and get immediate insight which may transform your way of thinking.


Which diseases are associated with HIV?

Type "HIV". Take a look at the "Top Categrories". Among others hepatitis and tuberculosis are mentioned. Clicking on tuberculosis retrieves the relevant articles including statements such as "Despite the synergy between the human immunodeficiency virus (HIV) and tuberculosis (TB) epidemics, the public health responses have largely been separate".


Concepts of the "What"-category recently selected appear in yellow color (in the example of tuberculosis), other selected concepts appear in green color (in the example of HIV). All other concepts found in the text are also highlighted.

Description, synonyms, and Wikipedia links are shown by moving the cursor over the term. statistics of "What"-concepts are available on the top of the page.


If you are interested in articles about HIV, which are not related to hepatitis, you have to exclude the concept hepatitis.

Customize your view! Simply hide or show concepts you do or you do not want to see. From simple keywords to complex advanced searches! GoPubMed offers a wide spectrum of possibilities. See how context changes search results.



Where are leading centers and who are scientists for liver transplantation in Germany?

Type "Liver Transplantation"[mesh] Germany[geo]" or type "Liver Transplantation"[mesh] (using the autocompletion feature), go to the "Where"-category and click on Germany. At the top of the "What"-category the result shows the top author "Neuhaus P" and the city is "Berlin". Prof. Peter Neuhaus works at the Charite Hospital in Berlin, Germany and is a leading specialist in the field.


By clicking on "Top Author" his profil is shown.

A Contact link is available near the profil. Your contact message will be checked by the GoPubMed Team and later it will be sent to the author.

Errors in the author profile can be reported using the "correct" link.


Do you know which topics Craig C. Mello and Andrew Z. Fire are working on?

Search for "Mello C[au] Fire A[au]". Now inspect "What"-, "Where"-, "Who"- and "When"-categories!

Following the top categories the answer is automatically extracted:

  • Caenorhabditis elegans
  • RNA, Double-Stranded
  • RNA interference

Craig C. Mello and Andrew Z. Fire obtained the Nobel Prize in Physiology or Medicine 2006"for their discovery of RNA interference - gene silencing by double-stranded RNA"


Co-Authors, localities and representative journals can be examined at a glance.

Usability

Convenient tools to work with your findings allow flexible screens and helpful synopsis.

Export articles in Endnote, BibTeX, text plain, XML, RDF or FullText.

Links to Wikipedia the concepts which are found in this paper.

Affiliation of this paper.


Autocompletion

By starting to type 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.

More Examples of Use

Exploring “cellular components

Which cellular component is the protein rab5 associated with?

  • Search for “rab5
  • Following the frequent term “endosome ”, GoPubMed shows that more than 50% of all retrieved papers containing your query “rab5 ” are related to this “cellular component ”.

Exploring diseases

Which disease is rhodopsin involved in?

  • Search for “rhodopsin ” and in just one mouse click on “Diseases ” your question is quickly found.
  • The group of more important diseases related to rhodopsin are shown under this ontological category.
    • Retinitis
    • Retinal Degeneration
    • Retinitis Pigmentosa

More than 4000 Diseases can be explored und related with your query.

Exploring “biological processes

Which biological processes are inhibited by aspirin?

  • Search for “aspirin inhibits ”.
  • By inspecting the most frequent term “biological processes ” you can very quickly understand that “cyclooxygenase pathway ” is the pathway related to this biological process. GoPubmed found more than 30% papers verifying that “cyclooxygenase pathway ” is inhibited by aspirin.

Exploring “organisms

Which organism is mostly involved in toluene degradation?

  • Search for “toluene degradation ”.
  • GoPubMed knows that “Pseudomonas ” and “Bacteria ” are involved in toluene degradation.

Exploring “proteins

Which proteins are most relevant for sickle cell anemia?

Sickle cell anemia defined as “a disease characterized by chronic hemolytic anemia, episodic painful crises, and pathologic involvement of many organs ” is mostly related to Blood Proteins, Hemeproteins and Membrane Proteins.

With GoPubMed 2500 Proteins can be related to your query.