OReFiL: an Online Resource Finder for Lifesciences

What is OReFiL?

OReFiL stands for Online Resource Finder for Lifescience. It facilitates a search for online resources that are introduced in peer-reviewed papers. You can search by MeSH terms or author names in addition to free words. OReFiL extracts all URLs from MEDLINE abstracts and PubMed-indexed BioMed Central full-papers (implementation or availability sections), and indexes them with MeSH terms and author names.

What is the benefit of using OReFiL?

1. OReFiL returns up-to-date query-relevant online resources that is introduced in peer-reviewed papers.
2. Users can search for online resources not only by free words, but also by MeSH terms or author names.
3. Users can easily verify each hit resource by following the links to its corresponding PubMed entry, webpages having a link to that of the hit resource, or papers citing it through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar.
4. Users can quickly confirm the existence of an online resource webpage.

Tips

• Query can be any keywords. Each keyword can be modified to specify a context by adding the following modifiers after it:
  • .tiab for titles and abstracts (e.g.,apoptosis.tiab),
  • .auth for author names, and
  • .mesh / .majr / .noexp for MeSH terms.
  An example is Proteins.mesh (a mesh term followed by ".mesh" is for all kinds of MeSH headers, by ".majr" for those of MeSH headers of major topics with semantic expansion, or ".noexp" for those without semantic expansion).
• A multiword keyword can be expressed using the #1 operator with parentheses such as #1(text mining) or #1(Sequence Analysis).
• Boolean "AND" operator can be used using the #band operator with parentheses such as #band(pathway apoptosis).
• Boolean-AND-like language-model-based search can be done using the #filreq operator with parentheses such as #filreq(Software.noexp #1(sequence analysis)). In this example, OReFiL only considers those resources whose MEDLINE entries have the MeSH term "Software" and rank them according to the query #1(sequence analysis).
• Punctuations are ignored. So, "Databases, Protein" and "Databases Protein" are identical.
• Non-alpha-numericals except for query operations are ignored. For example, "Variation (Genetics)" and "Variation Genetics" are identical.
• Detailed usage of this system can be learned at this video tutorial.
• This system uses Lemur Toolkit (Indri), and the query language can be learned here.
• Detailed information of this system can be found at BMC Bioinformatics 2007, 8:287.
  

Last index update: Dec 6, 2018