COMING SOON TO YALE: Ingenuity Pathway Analysis (IPA) and MetaCore for the Analysis of The Omics Data

27 March 2015 - 1:07pm -- Rolando Garcia-Milian

The Cushing/Whitney Medical Library is coordinating – for the use of the Yale community- the license for two concurrent seats (only two users at a given time) of Ingenuity Pathway Analysis, and a campus-wide license for MetaCore. These, along with BIOBASE (already available at Yale) are suites of online commercial software for the analysis of omics data.

Ingenuity Pathway Analysis (IPA) is supported by a manually-curated knowledge base of scientific relationships obtained from peer-reviewed journals, public and private biomedical databases. This knowledge base includes contextual details such as species specificity, cell type/tissue context, site and type of mutations, direction of change, post-translational modification sites, epigenetic modifications, and experimental method. With IPA you can identify relevant biomarkers, contextualize metabolomics data, analyze RNA-seq, proteomics, toxicogenomics, and transcriptomics data, perform network analysis among others.

Software-assisted identification of putative biochemical networks by Ingenuity Pathway Analysis

MetaCore (Thomson Reuters) is also a based on a manually-curated database of transcription factors, receptor/ligands, kinase, drugs, etc. It contains curated information on species-specific directional interaction between protein-protein, protein-DNA, protein-RNA, drug targeting, metabolic pathways, etc. MetaCore can be used for the functional analysis of the NextGen sequence data, CNV, microarray, proteomics, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data.

Map of BCR-pathway as shown by a MetaCore analysis

For additional questions please contact:

Rolando Garcia-Milian

Biomedical Sciences Research Support

Cushing/Whitney Medical Library

67th Annual Associates Lecture

25 March 2015 - 10:14am -- Katie Hart

Please join us for the 67th annual lecture of the Cushing/Whitney Medical Library Associates on April 8, 2015 at 4pm in the Historical Medical Library. This year's speaker is Dr. Unni Karunakara, Senior Fellow, Jackson Institute for Global Affairs and Resident Fellow, Morse College, Yale University and past international president of Médecins Sans Frontières. Dr. Karunakara's lecture is entitled "Humanitarian Duties and Action."


National Center for Biotechnology Information workshops broadcasted from the University of Michigan Medical Center

20 March 2015 - 10:53am -- Rolando Garcia-Milian

The Yale Medical Library will be hosting a National Center for Biotechnology Information workshop series (broadcasted from the University of Michigan Medical Center). Please register (next to each workshop title) since seating is limited

Navigating NCBI Molecular Data through the Integrated Entrez System and BLAST (May 5, 9:00am - 11:30am EDT) REGISTER HERE

Gene Expression Resources at the NCBI (May 5, 1:00pm - 3:30pm EDT) REGISTER HERE

Human Genes, Variation, and Medical Genetics Resources (May 6, 9:00am - 11:30am EDT) REGISTER HERE

NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (May 6, 1:00pm - 3:30pm EDT) REGISTER HERE

Each workshop consists of four 2.5-hour hands-on sessions emphasizing a different set of NCBI resources. Each session uses specific examples to highlight important features of the resources and tools under study and to demonstrate how to accomplish common tasks. Attendees will learn among others:

  • The content of the sequence databases and uses these as exemplar Entrez molecular databases.
  • The importance of derivative data such as NCBI Reference Sequences (RefSeqs) and sequence-related Entrez information hubs such as Taxonomy, HomoloGene and Gene.
  • Aspects of the Entrez interface to collect and download a specific set of records, to narrow the search, and to use the pre-computed relationships available in the Entrez system to find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information.
  • The practical aspects of working with NCBI BLAST, the most popular sequence similarity service in the world.
  • How to use the features of the updated service including direct access from the Entrez sequence databases.
  • The integrated databases to find phenotypes, literature, sequences (genome, mRNA and protein), and variations.
  • How to map variations onto genes, transcripts, proteins, and genomic regions.
  • Gain experience using additional tools and viewers associated with Entrez. These include the Graphical Sequence Viewer, the Variation Viewer, Gene View in dbSNP, and the 1000 Genomes Browser.

NCBI's Entrez as a discovery system. Image courtesy of Dr. Peter Cooper, NCBI.

MLA awards 2015 Louise Darling Medal to Yale partner HINARI

17 March 2015 - 8:37pm -- Andy Hickner

The Medical Library Association (MLA) has announced that it has awarded its Louise Darling Medical for Distinguished Achievement in Collection Development in the Health Sciences to the HINARI Access to Research in Health Programme for 2015. HINARI partners with publishers around the world to deliver scholarly health information and content (articles, books, and databases) to developing countries around the world who otherwise could not afford these resources. Under the guidance of Nathan Rupp, the library’s Head of Collection Development and Management, the Cushing/Whitney Medical Library plays and essential role in supporting HINARI by helping update publisher content in the HINARI database. HINARI is headquartered at the World Health Organization in Geneva and is part of the Research4Life (R4L) series of programmes which also includes AGORA (agriculture), ARDI (applied technology), and OARE (environment). Yale University Library is a Founding Partner in Research4Life, starting with the launch of HINARI in 2002. 

Remote Access to PubMedCentral Unavailable

17 March 2015 - 4:33pm -- Andy Hickner

Update 4pm EST, March 18:  PubMed Central access has been restored. 

The Medical Library’s access to PubMedCentral is currently unavailable to remote users, although it is available via the Yale wired network on campus. Library staff are currently working with Yale’s IT department and the vendor to fix this problem and we will post another notice when it has been resolved. We apologize for the inconvenience. 

Free CME courses now available through Henry Stewart Talks

12 March 2015 - 12:26pm -- Andy Hickner

Yale Affiliates can now earn CME credits for listening to the Biomedical and Life Sciences Collection of the Henry Stewart Talks. Yale University and YNHH, as well as individual faculty and staff, spend hundreds of thousands of dollars to fulfill these requirements.

On the home page (linked above) you should see that you now have CME available. (If you don't, you may need to log in to the Yale VPN.) Anyone at Yale wanting to fulfill their CME credits as required by the American Medical Association, or other professional organization, can click to register.  

Access to Electronic Books and Journals via ClinicalKey

5 March 2015 - 9:29am -- Nathan Rupp

Cushing/Whitney Medical Library provides access to ClinicalKey, a clinical search engine that provides easy access to over 1,100 electronic books and over 600 electronic journals across over thirty medical specialties. It includes titles like Boron’s Medical Physiology; Bolognia’s Dermatology; and Goldman’s Cecil Medicine, along with the Clinics of North America series, all of which can be accessed via Orbis, the Yale University Library catalog ( and the Medical Library’s e-book and e-journal lists (

Clinicians may find ClinicalKey's evidence-based point-of-care tool First Consult particularly useful. 

If you have any questions about ClinicalKey, please contact your personal librarian or departmental library liaison.

New guide to Open Access initiatives supported by Yale Library

27 February 2015 - 12:28pm -- Andy Hickner

There is a new guide to Open Access initiatives supported by Yale Library.

The page lists OA programs in two categories:

  • those that provide Yale authors discounts on open access publication fees
  • OA initiatives supported through library memberships

The guide will be updated as YUL joins additional OA programs.

For further reading on Open Access, we recommend the SPARC OA page, Wikipedia entry, or one of several books the library holds on the subject.   

Database trial - Wiley StatsRef: Statistics Reference Online

27 February 2015 - 12:07pm -- Andy Hickner

We are happy to announce a trial of Wiley StatsRef: Statistics Reference Online.  This database covers a variety of subjects with statistics being the thread throughout.  Please click here for a  Topic search and here for the Article A-Z search.  If you browse by topic, you’ll see the breadth included as noted below. 

  1. Actuarial Science
  2. Statistics in Biological and Medical Sciences
  3. Statistics in Business and Finance
  4. Statistics in Engineering
  5. Statistics in Environmental Sciences
  6. Statistics in Physical Sciences
  7. Statistics in Social and Behavioral Sciences

The database:

  • Comprises over 6,000 articles from across the breadth of Wiley's extensive reference resources in statistics - equivalent to over 30 volumes in print
  • Over 30,000 new cross-references and related article links added to greatly enhance the user experience by providing easy access to increased context and background
  • Browse by article or topic
  • Fully searchable
  • Regularly updated with new and revised content
  • New bespoke taxonomy created for a more intuitive and efficient user experience
  • The new structure and article enhancements create a genuinely stand alone, self-contained work covering all aspects of the subject in a single product

Articles in Wiley StatsRef have been carefully selected from the following eight products in Wiley’s existing online reference work portfolio, with thousands of new cross-references and links to related articles added to hugely enhance discoverability and ease of navigation:

  • Encyclopedia of Actuarial Science
  • Encyclopedia of Biostatistics
  • Encyclopedia of Clinical Trials
  • Encyclopedia of Environmetrics
  • Encyclopedia of Quantitative Risk Analysis and Assessment
  • Encyclopedia of Statistical Sciences
  • Encyclopedia of Statistics in Behavioral Science
  • Encyclopedia of Statistics in Quality and Reliability

Send feedback to Gwyneth Crowley at


Subscribe to RSS - blogs