BW FAQ - Literature

-> LITERATURE

                -> LIT1...know in which publications my own papers are cited ? (last update Feb. 7, 2006)
                -> LIT2...see if patents exist which are related to a molecule of interest ? (last update Feb. 7, 2006)
                -> LIT3...perform a PubMed query using automatically all synonyms of my gene name of interest ? (last update Feb. 23, 2006)
                -> LIT4...see the authors which are most active in a specific field and their preferred journals ? (last update Feb. 23, 2006)

LIT1...know in which publications my own papers are cited ? (last update Feb. 7, 2006)

    Tip! Google Scholar enables you to search specifically for scholarly literature, including peer-reviewed papers, theses, books, preprints, abstracts and technical reports from all broad areas of research. Just as with Google Web Search, Google Scholar orders your search results by how relevant they are to your query, so the most useful references should appear at the top of the page. Google Scholar also automatically analyzes and extracts citations and presents them as separate results, even if the documents they refer to are not online. This means your search results may include citations of older works and seminal articles that appear only in books or other offline publications.
    Google Scholar can be used very effectively as citation tracking service, as publications which were cited by others show a link to these references, like "Cited by 27". Thereby, you may quickly list all publications which refer to your paper of interest.

LIT2...see if patents exist which are related to a molecule of interest ? (last update Feb. 7, 2006)

        When starting to work on a specific molecule of interest, it may be highly interesting to know whether patents exist which relate to this molecule. For this purpose, there are special patent databases available which can be queried using various search terms.

    The European Patent Office (EPO) grants European patents for the contracting states to the European Patent Convention (EPC). It is the executive arm of the European Patent Organisation. esp@cenet is Europe's network of patent databases. It is a free internet service from the European Patent Organisation. Use it to search 45 million patent documents. To use esp@cenet, click on the "Access esp@cenet" link, which then provides selected searches at the EPO, at the European Commission, or at any national patent office (note that different languages are supported !). In most cases, a "Quick Search" is sufficient to retrieve the desired documents. For this purpose, you have to specify the database ("worldwide", or EP, or Japan, and more), the type of search (words in title or abstract, or persons and organisations), and enter your search term(s). You will retrieve an overview, and the full description (including even the original document supplied by the submitter) of the patent. Note that It is not possible to print or download the whole documents "in one run" but you may print one page after the other using the small "Print" command on top of the page (NOT the "Print" command of your PDF-software). Likewise, you may download one page after the other as individual PDF-files. Interestingly, a test search at "Patent Abstracts of Japan" revealed documents which were not available via the "worldwide" database option, so it may be worth to check several of the databases listed.

    SRS (Sequence Retrieval System) is a powerful tool for database search via keywords, which offers an alternative approach to retrieve patent data. Please refer also to the main SRS description at the "Sequence retrieval" page for general information. At the "Library selection page", there are several libraries related to patent information, like "PATENT_DNA", a library of patented DNA sequences from the EPO, or "Patent_Abstracts" from ESPACENET. Simply select these databases and enter your search terms at the "Quick Search" field or at the "Query Form".

LIT3...perform a PubMed query using automatically all synonyms of my gene name of interest ? (last update Feb. 23, 2006)

        This question addresses a central problem in gene / protein specific literature searches, as in most cases several synonyms exist for a gene name. For example, a query in PubMed using "XIAP" retrieves a different number of entries than a query using its official gene symbol "BIRC4".

    Tip! PubReMiner is a tool for PubMed query building and literature mining, developed at the Academic Medical Center (AMC) in Amsterdam, Netherlands. PubReMiner will query pubmed with your specified searchquery, get all abstracts and generate 3 frequency tables. The first table will show you journals in which your query is published the most. The second table will show you the authors which are most active in the field of your query. The last table will show you words that have been used most in the title and abstract of the articles. These "keywords" can be added to your query, and will thus make sure that your refinement still generates results. When you are satisfied with the query, you can jump to pubmed and view the results.
    Note that in order to address this specific question, PubReMiner provides a specific "Lookup gene" query field. Entering a gene name here will automatically generate a query using ALL synonyms.

LIT4...see the authors which are most active in a specific field and their preferred journals ? (last update Feb. 23, 2006)

        This question is often asked when a researcher enters a new scientific field and wants to get an overview of people who already published on this topic, and their preferred journals.

    Tip! PubReMiner is a tool for PubMed query building and literature mining, developed at the Academic Medical Center (AMC) in Amsterdam, Netherlands. PubReMiner will query pubmed with your specified searchquery, get all abstracts and generate 3 frequency tables. The first table will show you journals in which your query is published the most. The second table will show you the authors which are most active in the field of your query. The last table will show you words that have been used most in the title and abstract of the articles. These "keywords" can be added to your query, and will thus make sure that your refinement still generates results. When you are satisfied with the query, you can jump to pubmed and view the results.