Alternative Tools for Mining The Biomedical Literature

Transcription

1 Yale University From the SelectedWorks of Rolando Garcia-Milian May 14, 2014 Alternative Tools for Mining The Biomedical Literature Rolando Garcia-Milian, Yale University Available at:

2 Alternative Tools for Mining The Biomedical Literature Rolando Garcia-Milian Curriculum and Research Support Cushing/Whitney Medical Library, Yale University

3 Contents QUERTLE... 3 Quertle coverage... 3 Creating an account... 3 Example 1 Single term query... 5 Filters... 6 Example 2 - Two term query... 8 Example 3 - Three term query... 8 Saving and exporting your results and searches Semantic Medline (SemMed) NextBio (Literature) NextBio Coverage Creating an account Searching NextBio Literature Saving and exporting your results and searches References

4 QUERTLE Quertle "query". + "article" - The full version of Quertle was launched on November 18, Online free to use - Understand the differences between NO (nitric oxide) and no (negative) - Contains about 300 million relationships triplets (subject-verb-object) within the biomedical literature. A relationship is a Subject-Verb-Object triplet representing an assertion by the author- they are order independent ( e.g. streptozotocin induces diabetes or diabetes is induced by streptozotocin ) Quertle coverage -MEDLINE/PubMed -Full-text documents from BioMed Central and Open Access articles from PubMed Central. -NIH RePORTER database of grant applications -National Library of Medicine's TOXLINE database of biochemical, pharmacological, physiological, and toxicological effects of drugs and other chemicals. -News (as reported by FierceMarkets Life Sciences and Health Care) -Scientific whitepapers and research posters submitted to Quertle (contact us about submitting yours). Creating an account Begin by clicking on Log in or Create an Account link if you do not have one. In order to save your searches- and if interested in receiving weakly alerts-, log in or create an Account. It also allows you to see My Library link next to your results. 3

5 In order to save your searches and see if an article is available at your institution, sign in and go to your Quertle by clicking on the link on top of the page. Signing in allows you to save your searches. This can be done by click on Save Search+Filters once you get your results. If you want to receive weekly alerts for new documents based on your search criteria, check on the Alert box under the Saved Searches tab. To run a saved search, just click on the blue icon under the Run tab. 4

6 In order to see if the article is available at your institution, go to My Profile tab and select your institution from the Organization drop-down menu. Example 1 Single term query Type BRCA1 on the search box- as you begin typing, Quertle will offer a list of options (autocomplete function)- select the first one BRCA1. 5

7 The Focused Results tab provides documents that contain relationships in which your search term is present. If the document contains more than one relationship, the five most relevant ones will be displayed. The Broader Results tab contains documents based on your search term as keyword. Your search term is highlighted in yellow. Filters Results can be further filtered by date ( Published Within ), Publication Type, and Key Concepts which are the most relevant concepts found within the relationships. 6

8 From the key concept list, select regulate (action concept) by clicking on it. The results will automatically update. The selected key concept will be bolded in the results display. 7

9 Example 2 - Two term query Type BRCA1 EGFR inside the search box and click on the Search button. In this case, searching for these two objects will find documents containing BRCA1 and EGFR connected by an action. It would be the same as searching BRCA1 what EGFR. Example 3 - Three term query 8

10 Queries can be created by using Power Terms (classes of related concepts). For a complete list of Power Terms, click on Power Terms link right below the search box. A new window will appear- click on Full Lists of Power Terms link. In this case we will search by using a query consisting of "object1 action object2" in order to find documents with the specific relationship. Type BRCA1 regulates $Protein inside the search box in order to find out what proteins are regulated by BRCA1. 9

11 In addition, you can use the Key/General Concepts Filters to narrow your search. For example, in order to know what protein activity is regulated by BRCA1- click on the activity (action concept) link under General Concepts filter. 10

12 Saving and exporting your results and searches Once you have finished your query, you can save it (including the filters used) by clicking on the Save Search+Filters link. This required to be logged in to your Quertle account. Click on the link Search Saved in MyQuertle, to view your saved searches. 11

13 If you want to receive weekly alerts for new documents based on your search criteria, check the Alert box under the Saved Searches tab. To run a saved search, just click on the blue icon under Run Select the document you want to Export. You can select individual documents by checking the boxes next to the document number. 12

14 You can select all the documents by checking the box at the top of the results page. Select all (29) references and RIS (Research Information System) format, click on the Export button and save the results. RIS format can be open by most of the reference management systems (e.g. EndNote, Refworks, Mendeley, Zotero, etc. 13

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16 Semantic Medline (SemMed) It can be accessed at In order to search PubMed using SemMed, the user needs to have a UMLS (Universal Medical Language System) license/account. Please create a UMLS account if you do not have one. It might take up to three business days for your request to be processed. UMLS website: Log in with your UMLS account following the link above. 15

17 Insert you query on the search box. For this example (CPY2C9 AND cancer). Set the number of citations to be retrieved to (500 by default). Click on the Search button. By clicking on the Show button you can use additional PubMed limits (we won t use Limits for this example). You can also change the time period of your search by modifying the Star and End dates (we will leave the default values as is). Search results appear at the bottom of the page as a brief display of the authors, title, and PMID (PubMed Unique Identifier.) 16

18 Click on the Summarization tab. From the Summary Type drop-down menu select Pharmacogenomics. From the list Select a UMLS concept to summarize on choose the first one (CYP2C9 gene), check More Relations box, and click on Summarize button. 17

19 Results will be shown as a network graph with nodes and edges. The concept you selected from the list Select a UMLS concept to summarize on (in this example CYP2C9 gene) will be displayed in the center of the graph. The SemMed graph window contains two sections: a viewer pane and a tool pane. The viewer pane displays the semantic connections diagram ( graph ). The tool pane contains several tabs which help the user navigate through the information in the viewer pane 18

20 Select the Radial layout from the Layout menu at the bottom of the left corner. In the tool pane, you can use the Search option for searching concepts inside the graph. For example, click on the Search tab (in the tools pane), type carcino* into the search box and click on the Search button. 19

21 Click on Ovarian Carcinoma from the list of results. The graphical interface will be re-centered on this concept. 20

22 By clicking on any arrow you will see the reference that supports the relationship between a pair of concepts. Click on the green arrow connecting the Anti-Inflammatory Agents, Non-Steroidal with Ovarian Carcinoma concept, the Information tab in the tool pane will open showing the Relationship Information. Click on the Citations button to view supporting reference for this relationship. A new window will open showing a highlighted sentence from where the relationship was extracted. 21

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24 NextBio (Literature) Literature is a NextBio application that query PubMed. It extracts key biomedical terms and sorts the results in order of relevance as a tag cloud. Sizes of the resulting terms reflect their relevance to the search. Easier to refine search For Literature searches, NextBio uses: - Ontology with relationships between terms, synonyms, as well as a term hierarchy; - Domain-specific stop-word list (e.g. learning can be a stop-word in the domain of education but a keyword in computer science) and analyzer that emphasizes ontology terms; - Overall authority of the journal in which the paper was published - Date of publication. NextBio's auto-complete and tag cloud terms come from the following ontologies and indexes: - Genes and SNPs Entrez Gene, UniGene, Ensembl, RefSeq, GenBank, and dbsnp - Phenotypes: SNOMED Clinical Terms - Tissues: MeSH - Compounds: MeSH, PubChem - Biogroups: Gene Ontology, MSigDB, InterPro, TargetScan - Organisms: MeSH NextBio Coverage PubMed (23 million) Full-text publications from PubMed Central (2.8 million) Clinical trials from ClinicalTrials.gov Elsevier full text journal articles (23 million - available to NextBio Enterprise customers who subscribe to ScienceDirect) News - sourced from publicly available biology- and health-related news publications 23

25 Creating an account Sign up or log into NextBio Research in order to use the features available to registered users. Searching NextBio Literature Click on the Literature icon on top of the page to open the Literature application. 24

26 Enter your query on the search box. Type stroke - as you begin typing NextBio will provide a list of terms pulled from different controlled vocabularies/ontologies. Select phenotype > Cerebrovascular accident :: Stroke from SNOMED_CT 25

27 Your search results will be at the bottom of the screen under the tag cloud. Tags are listed alphabetically within the tag cloud; tags that appear in a larger typeface are more strongly associated to your search term. To see a more comprehensive tag cloud, select 200 or 1000 from the drop-down menu to the far right of the filter options bar. Note: Including more results will also increase computing time. For this example, we ll leave the default value as is (50) 26

28 You can filter your search by: affiliation, author, biogroup, Medical Subject Headings, FDA-approved drugs, organism, etc. Click on affiliation next the filter terms bar to see main institutions working on a the topic Click on MeSH annotations to see the Medical Subject Headings associated with your search term. Click on Humans tag to restrict the query to this organism. Notice how the number of results diminishes from 153,213 to 122,791. The new applied filter was added to the filter box located below the tag cloud. 27

29 Click on FDA drugs to see those FDA-approved drugs associated with your search term. Click on clopidogrel o apply this filter. Notice how the new filter is added to the filter box and number of results diminishes to 1,474 28

30 Click on the gene and proteins filters and mouse-over the CYP2C19 term. A box containing additional information on this term will appear. Notice that this is a Homo sapiens term. If you mouse over Cyp2c70, the information box will reveal that this is a Mus musculus term. Click on the CYP2C19 term. Your results will go down to 22 29

31 By clicking on the title of the first result you will be taken to a record containing the publication title, authors, abstract, citation, MeSH tags, etc, and a tag cloud of the article with word frequencies. 30

32 Click on the View Full Text button to have access to the full text. Saving and exporting your results and searches The free version of NextBio only allows you to forward or bookmark the URL of the paper. Highlighted 31

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34 References General Islamaj Dogan R, Murray GC, Névéol A, Lu Z. (2009) Understanding PubMed user search behavior. Database (Oxford) Hoffmann R, and Valencia A. (2005) Implementing the ihop concept for navigation of biomedical literature. Bioinformatics 21(suppl. 2), ii252-ii258 Luz C (2011) PubMed and beyond: a survey of web tools for searching biomedical literature Database (Oxford) NextBio Resources FAQ Kupershmidt I, Jane Su Q, Grewal A, Sundaresh S, Halperin I, Flynn J, Shekar M, Wang H, Park J, Cui W, Wall GD, Wisotzkey R, Alag S, Akhtari S, Ronaghi M. (2010) Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data. PLoS ONE 5(9): e doi: /journal.pone Quertle Help Using Quertle Semantic Medline Rindflesch, T.C. et al. (2011) Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use, 31, pdf 33