Advanced search capabilities are available through the "Advanced" link above the input field.

The existing search methodology in GoPubMed has been refined and extended. Advanced Search makes it possible to filter publications by requiring certain terms or its children, journals, publications dates, etc.

This document provides help on

• using advanced search to refine the retrieval of documents
• focusing on articles mentioning or excluding certain GO and MeSH terms
• selecting certain publications, authors, etc.

by using the Advanced Search interface in a simple and intuitive manner.

A link on the "Where" category refers to "Advanced", where the interface for advanced features can be found. By clicking the link following options are available:

Number of papers:

The user can also alter the number of retrieved papers. By default the number of retrieved papers is limited to 1,000.

Querying the database PubMed:

Specific query terms can be chosen to appear in the:

• fulltext,
• anywhere,
• in the title or abstract,
• in the title.

The user is able to restrict searches to specific fields of the article such as:

• authors,
• affiliation,
• journals and review only, and
• date.

These fields have the same functionality like the syntax of PubMed: [ALL], [TIAB], [TI], [AU], [AD], [TA], review[PT], [PDAT].

Entering terms:

If a term of interest consists of more than one word it is necessary to put it into quotation marks: “Journal of Bacteriology” or the author “Zerial M”. Note that Journal names have to be entered with their full names.

To combine more than one query term in one query field, they can be connected with the

• AND (if both are required) or
• OR (if not necessarily both have to appear) operator.

In the example shown in the box below Advanced Search extracts articles containing reviews titles IGF AND "binding proteins" between the years 2000 and 2007.

If neither AND or OR are typed the machine chooses the AND.

By selecting hierarchical terms from the GO and/or MeSH ontologies, they are automatically inserted into activated fields. Children of required terms can be selected as well.

The following four options can be select:

• Include term
• Include term and children
• Exclude term
• Exclude term and children

To select a term you can

• either click down the ontology tree on the left hand side or
• type it to the ontology browser bar and the tree unfolds itself.

In the latter case you might scroll down the tree to find the exact term you want. Clicking the term automatically inserts it to the filtering mask and one of the four options mentioned above can be chosen.

Include term

All documents returned by the search contain exactly a GO or MeSH Ontology term or one of its synonyms.

Searches containing more than one term from the ontology return only documents containing ALL of this terms (Boolean AND) and your query.

A search for Include terms "endosome" and "proteins" selects all PubMed abstracts that contain:

• endosome or one of its synonyms
• proteins or one of its synonyms
• your query.

Include term and children

All documents returned by this search contain either exactly this term (or one of its synonyms) or one of its child concepts (or their synonyms).

If more than one GO or MeSH term and children are chosen, the returned documents will contain ALL these terms (or synonyms) or children (or synonyms) and your query.

A search for Include terms and children “endosome” and “proteins” selects all PubMed abstracts that contain:

• Endosome
  • OR early endosome
  • OR late endosome
    • OR multivesicular body
• AND Proteins
  • OR Albumins
    • OR C-Reactive Protein
    • OR Conalbumin
  • OR Algal Proteins
  • ... more than 2500 Proteins names (including all synonyms)
• AND your query.

Exclude term

None of the documents returned by this search contain exactly this term nor one of its synonyms.

Searches containing more than one of this filters return only documents containing none of this terms (AND NOT).

Exclude term and children

None of the documents returned by this search contain exactly this term nor one of its synonyms nor do they contain one of the child concepts nor their synonyms.

Searches containing more than one of this filter return only documents containing none of these terms and children (or synonyms of all).