The BioCyc Microbial Genomes and Metabolic Pathways Web Portal is coming to the University of Cincinnati.
Beginning August 31st, researchers can access the full suite of databases in the BioCyc Database Collection. The BioCyc web portal from SRI International contains genome and metabolic-pathway information for over 10,000 microbes. BioCyc encyclopedias are unique in integrating a diverse range of data and providing a high level of curation for important microbes. BioCyc Pathway/Genome Databases (PGDB) describe the genome of an organism, as well as its biochemical pathways and (for a small fraction of organisms) its regulatory network. BioCyc bioinformatics tools combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of its extensive and complex data.
BioCyc databases integrate extensive data for each organism, and provide platforms for analysis of large-scale datasets. BioCyc enables scientists to pursue several use cases:
- BioCyc is a massive encyclopedic reference on microbial genes, metabolites, and pathways that integrates information from many sources. Scientists consult BioCyc to save large amounts of time finding, understanding, and synthesizing material from the primary literature.
- BioCyc is a genome informatics and comparative genomics platform.
- BioCyc enables exploration of a vast set of biological networks.
- BioCyc provides gene-expression, metabolomics, and multi-omics analysis tools.
- BioCyc provides executable metabolic models for a small but growing set of organisms.
BioCyc Informatics Tools
- Search for genomes by name, taxonomy, phenotypic properties.
- Gene information page
- Retrieve amino-acid sequence and nucleotide sequence of arbitrary genome region.
- Query genes by gene name, accession number, sequence length, replicon position, protein properties (pI, MW, protein features, subcellular location, ligand), GO terms.
- Transcription-unit information page.
- Genome Browser depicts genomic regions at user-selected resolution with semantic zooming that reveals new features at higher resolutions. Visible features include pseudogenes, promoters, transcription-factor binding sites, repeats, terminators, nucleotide sequence. Zoom to sequence. Generate genome poster.
- BLAST search sequence-pattern search via patmatchMap SNPs to genes and show effects on translation.
Access this URL for more information about BioCyc databases and features: https://biocyc.org/intro.shtml.
Some additional links that may be helpful:
Guided tour: https://biocyc.org/samples.shtml
User guide: https://biocyc.org/PToolsWebsiteHowto.shtml
Data Sheet: BioCyc data sheet
Tiffany J. Grant, PhD
Interim, Assistant Director for Research and Informatics
Co-Leader, Research Services
Health Sciences Library
Office: (513) 558-9153
The Health Science Library is currently accepting applications for student assistants.
Positions are now open in the following Departments
- Winkler Center
Positions require a commitment of at least 6 – 15 hours per week. Some positions require a Federal Work Study Grant.
The library is located, near the main elevator banks, on the E level of the Medical Science Building, on the Medical campus.
Please fill out the Library specific application. Be sure to mark HSL as a preferred job site.
For questions concerning the Circulation Department,
For questions concerning the Winkler Center,
AHRQ National Guideline Clearinghouse (NGC) will no longer have funding after July 16th and so will no longer be available.
The NGC was originally created by AHRQ in partnership with the American Medical Association and the American Association of Health Plans (now America’s Health Insurance Plans [AHIP]), the NGC mission was to provide physicians and other health care professionals, health care providers, health plans, integrated delivery systems, purchasers and others an accessible mechanism for obtaining objective, detailed information on evidence-based clinical practice guidelines and to further their dissemination, implementation, and use.
For more information, see NGC Announcements.
The University of Cincinnati Libraries is pleased to present BenchSci to the UC research community.
Registration is free to all scientists with a uc.edu or affiliated institutional emails at https://www.benchsci.com
BenchSci is a online platform designed to help scientists find antibody data in publications. Their proprietary machine-learning algorithm was trained by PhD-level scientists to identify and understand the usage of commercial antibodies in the research literature.
When searching for a specific protein target, BenchSci curates published data in the form of figures to simplify the literature search process. The figures can then be filtered by specific experimental contexts cited in the paper such as techniques, tissue, cell lines, and more, to help users pinpoint antibodies that have been published under experimental conditions matching their study interest.
For more information about BenchSci, please refer to this article: https://blog.benchsci.com/7-features-to-find-antibodies
To learn how to navigate BenchSci, please watch this short video: https://youtu.be/EFaDwTtqlv4
For further inquiries or feedback, contact Maurice Shen, the Head of Academic Relations at BenchSci, at firstname.lastname@example.org
From making a diagnosis to tailoring treatment to an individual to someday curing disease, precision genomics is having a profound impact on healthcare.
Cincinnati Children’s Center for Pediatric Genomics and the University of Cincinnati launched Precision Genomics Midwest last year to bring genomic education to the Midwest. Often, clinicians and researchers don’t have the time to attend large national events, but they still need to learn about how genomics will be integrated into clinical care; about genomic technologies; and ongoing research in the field.
This one-day, free event – May 11 at the Kingsgate Marriott on the University of Cincinnati campus – is packed full of education on topics relevant to clinicians, researchers, pharmacists, genetic counselors, lab managers, nurses, and students.
- The whole day is free, including lunch.
- Two keynotes: Dan Kastner, MD, PhD, Scientific Director at the National Human Research Genome Institute, and Mike Murray, MD, Director of Clinical Genomics at Geisinger Health System.
- A new Bioinformatics track, with breakouts in clinical and research genome bioinformatics
- Break-out sessions including genomics in the clinic, pharmacogenomics, epigenetics, and ethical, legal, and social implications of genomics.
- A panel discussion on Innovative Genomic Therapeutics: Is Gene Editing or Gene Therapy the Answer to Curing Human Disease?
- The largest exhibitor fair in the Midwest, featuring more than 30 vendors and sponsors.
- A networking cocktail hour to finish the day.
Precision Genomics Midwest rapidly is becoming the Midwest’s premier precision medicine conference, by attracting regional attendance and national speakers while simultaneously showcasing talent from UC and Cincinnati Children’s. The inaugural year had nearly 360 registrants from more than 25 different institutions across the Midwest.
Cincinnati Children’s and UC College of Medicine are co-sponsoring the free conference. Other contributing partners include the Cincinnati Children’s Research Foundation, University of Cincinnati Libraries, and the Center for Clinical and Translational Science and Training.
PGM is free, but space is limited. For the agenda, registration, and exhibitor prospectus, go to www.cincinnatichildrens.org/pgm. For updates, follow @CincyKidsGenomX on Twitter.
UC Libraries moved to the new A-Z Databases List platform in July of 2017 just in time for the fall semester. The new platform provides easier access to UC Libraries databases and other databases available to UC students, faculty, and staff. Now that the spring semester is starting, take a closer look at the features of the A-Z Database List.
- Looking for a specific database like Scopus?
- What database names start with H?
- Want to find all the Biology databases?
- Looking for statistics?
Additional Features in the Column on the Right:
- New/Trial Database list: new resources are highlighted in the right column. Resources labeled as ‘Trial” will also be listed while being considered for future subscriptions.
- Report Database Errors: report a database problem using the form located below the new databases list.
- Icon Key: at the bottom of the right column is a key for the icons associated with each database entry.
So take a closer look at the A-Z Databases List! Use the list search and sort features to explore the 830 databases available to all UC students, faculty and staff.
How do to get to the A-Z Database List: Use the red search box on any library website.
Click on the Database tab, type the name of the database in the search field and click on go or click on the link that takes you directly to the list.
MedlinePlus is the National Institutes of Health’s Web site for patients and their families and friends. Produced by the National Library of Medicine, the world’s largest medical library, provides current and reliable information about diseases, conditions, and wellness issues.
- Health topics – symptoms, causes, treatment and prevention for over 1000 diseases, illnesses, health conditions and wellness conditions that are regularly reviewed and updated
- Drugs, Herbs and Supplements – information about prescription drugs, over-the-counter medicines, and herbs and supplements.
- Videos & Tools – videos on anatomy, body systems, and surgical procedures. Tools such as interactive tutorials and games, calculators and quizzes to test knowledge and health.
- Lab Test Information – what the lab test is, why it was ordered, how it will feel, and what the results mean.
- Medical Encyclopedia – The A.D.A.M. Medical Encyclopedia includes over 4,000 articles about diseases, tests, symptoms, injuries, and surgeries. It also contains an extensive library of medical photographs and illustrations.
- NIH MedlinePlus Magazine – reports on the latest NIH-supported research breakthroughs and features people from all walks of life talking about how they’ve handled health challenges.
- MedlinePlus Connect – an option for health providers to provide quality health information for patients via patient portals or the patient health record. MedlinePlus Connect is a free service of the National Library of Medicine (NLM), National Institutes of Health (NIH), and the Department of Health and Human Services (HHS).
Check out MedlinePlus and share it with patients, friends, and family.
What is PubMed Health? PubMed Health provides information for consumers and clinicians on prevention and treatment of diseases and conditions. It specialized in reviews of clinical effectiveness research, with easy-to-read summaries for consumers as well as full technical reports.
What else does PubMed Health provide?
- Systematic reviews of clinical trials showing what has been proven to work and what remains unknown
- Summaries and full texts of selected systematic reviews in one place published or updated from 2003
- Information for consumers and clinicians based on those reviews
- Methods resources collection that includes documents about the best research and statistical techniques for systematic reviews and effectiveness research
- Searches that run simultaneously in PubMed. A filter is used to identify all the indexed scientific articles at the National Library of Medicine (NLM) that might be systematic reviews
So take a moment to search and explore PubMed Health this freely available resource!
PubMed Health is a service provided by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
What is ORCID? ORCID stands for Open Researcher and Contributor ID.
Name ambiguity is deceptively tricky. You may share your name with another researcher, like the 10 Steve Smiths on the Center for Science Education’s “List of Steves.” You may change your name due to marriage or other reasons. You may simply use a different version of your name in different contexts, like former Democratic presidential candidate Bernard “Bernie” Sanders.
Enter ORCID: Open Researcher and Contributor Identification. You can think of ORCID as a Social Security number for researchers: a permanent, unique identifier that you can associate with your work to resolve any uncertainty about authorship. Nearly 2 million academics have signed up for an ORCID, in total laying claim to over 12 million documents.
Why do I need an ORCID?
- An ORCID is a unique identifier that allows you to associate your works with your name.
- Removes author ambiguity especially for individuals with common names or for people who change their name through the course of their career.
- Certain Publishers and Granting Agencies require that applicants have an ORCID. https://orcid.org/content/requiring-orcid-publication-workflows-open-letter
- Generating an NIH biosketch is easier with an ORCID.
- You can build an online profile of your scholarly works @ http://orcid.org
How do I get an ORCID?
You can register directly on the website http://orcid.org
Registering for an ORCID is free and takes around 30 seconds.
Upon registering, you can then access your ORCID account using your UC login. Visit the ORCID login page and click the Institutional Account button. Choose University of Cincinnati Main Campus. You will be prompted to link the two accounts.
The Donald C. Harrison Health Sciences Library (HSL) and UC Libraries provide services in addition to journals, books, databases and research guides. These services include:
- Monthly classes in the HSL Troup Learning Space – register to attend a variety of classes from REDCap, to Literature Searching, to presentation software like Prezi or Emaze, to citation management systems RefWorks and EndNote.
- Informatics Lab – reserve this collaborative hands-on learning space where you can work with software like SPSS, SAS, R, Matlab, Satscan, Python, Photoshop and more. Get assistance with statistical work or meet with a Writing Center tutor.
- Winkler Center Lucas Board Room – reserve this space for meetings or events
- HSL Computer Lab – use the computers available or your own laptops/devices, get assistance with setting up secure wireless, email and more.
- Poster Printing – located in the HSL and available to all Academic Health Center students.
- Data Management Planning – information about DMP. Contact us for assistance with managing research data, preparing a data management plan for a grant submission and more.
- Scholar@UC – a digital repository that enables the UC community to share research and scholarly work with a worldwide audience.
Want to know more?