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Semantic Software Lab
Concordia University
Montréal, Canada

OMM Query

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1. Background

OMM Query is our online search interface for an index of full-text research papers from the complete PMC Open Access Corpus (nearly half a million documents), mined for mutation information with Open Mutation Miner (OMM) [1] and OrganismTagger [2]. It can be accessed using the Mímir query language, combining entity annotations with their features with plain text (see below for some examples).

Note that you can index your own set of documents through OMM and install a local query server, if you want to mine a different set of documents for mutation impact information: all software used in this process is freely available under open source licenses. Besides the web interface, it is also possible to query the Mímir server through a RESTful API. If you need paid support for customizing your own OMM installation, please contact us for possible options.

2. Example Queries

OMM-Query ExampleOMM-Query Example
Here are some queries you can try out (paste the text in blue typewriter typeface into the search box). For a full description of the Mímir query language, please refer to the documentation. In the result list, you can click on the PubMed ID to see the paper directly in PMC, or click on the "cached" link to see the detected entities highlighted in the full-text:

How many mutations did you find in the PMC OAC?
What about organisms?
How many of the mutations have Alanine as the wild-type?
{MutationMention wildType="A"}
How many mutation impacts are there?
How many of these impacts affect the protein property affinity?
{Impact} OVER affinity
Show me all impacts due to the mutation "A43T":
{Impact mutation="A43T"}
Queries can be nested: Show me all impacts that increased the thermal stability of a protein:
{Impact} OVER increase & {ProteinProperty class="ThermalStability"}
Show me all detected sentences containing relations between impacts and protein properties:
Show me all detected sentences containing relations between protein properties and physical quantities:
Additionally, you can perform a plain full-text search, which can also be combined with the annotations: Show me all sentences that contain the phrase "we have shown"
{Sentence} OVER we have shown

3. Online Query Interface

Click the link below to open the query window and enter your query. In the result list, clicking on the PubMed ID will bring you to the online version of the article, whereas clicking on "cached" will show a local copy (unformatted text only) with the query results highlighted (note: you need to allow pop-ups).

Open OMM query page in a new window


  1. Naderi, N., and R. Witte, "Automated extraction and semantic analysis of mutation impacts from the biomedical literature", BMC Genomics, vol. 13, no. Suppl 4, pp. S10, 06/2012.
  2. Naderi, N., T. Kappler, C. J. O. Baker, and R. Witte, "OrganismTagger: Detection, normalization, and grounding of organism entities in biomedical documents", Bioinformatics, vol. 27, no. 19 Oxford University Press, pp. 2721--2729, August 9, 2011.