Welcome to our bioscience portal, where we feature content and news about our program in biosciences.

Our goal for the program is two fold:

  • to introduce the bioscience community to open, web-based annotation
  • to explore specialized uses within the biosciences to inform future development

Attention Biocurators: Interested in controlled tagging using Hypothesis? We have developed some prototypes that allow Hypothesis to tag with controlled vocabularies and ontologies. We’d like your feedback. If interested, contact us.

Also, many in the Hypothesis community are developing tools using Hypothesis that handle more specialized use cases. See what they are up to and add your own.

Whether you are a researcher, student, educator, journal editor, funder or just a fan of bioscience, we think that Hypothesis can become an essential part of your work.

Advisory board

Russ Poldrack

Neuroimaging, Stanford University

Russell A. Poldrack is a professor of Psychology and head of the Center for Reproducible Neuroscience at Stanford University. Prior to his move to Stanford, he served as Director of the Imaging Research Center and Professor of Psychology and Neurobiology at the University of Texas, Austin. He previously held the Wendell Jeffrey and Bernice Wenzel Term Chair in Behavioral Neuroscience at the Neuroscience Faculty at UCLA. A champion of open and reproducibile neuroimaging, he heads the Cognitive Atlas project and OpenfMRI. He recently released the MyConnectome dataset, where he scanned and sequenced himself weekly for 1 year.

Andrew Su

Molecular biology, Scripps Research Institute

Andrew Su is Associate Professor at the Scripps Research Institute in the Department of Molecular and Experimental Medicine (MEM). His research focuses on building and applying bioinformatics infrastructure for biomedical discovery. His research has a particular emphasis on leveraging crowdsourcing for genetics and genomics. Representative projects include the Gene Wiki, BioGPS, MyGene.Info, and Mark2Cure, each of which engages “the crowd” to help organize biomedical knowledge. These resources are collectively used millions of times every month by members of the research community, by students, and by the general public.

Geoffrey Bilder

Scholarly Communications, Cross Ref

Geoffrey Bilder is Director of Strategic Initiatives at CrossRef, and has over 16 years experience as a technical leader in scholarly technology. He co-founded Brown University’s Scholarly Technology Group in 1993, providing the Brown academic community with advanced technology consulting in support of their research, teaching and scholarly communication. He was subsequently head of IT R&D at Monitor Group, a global management consulting firm based in Cambridge, Massachusetts. From 2002 to 2005, Geoffrey was Chief Technology Officer of scholarly publishing firm Ingenta, and just prior to joining CrossRef, he was a Publishing Technology Consultant at Scholarly Information Strategies, where he consulted extensively with publishers and librarians on emerging technologies and how they may affect scholarly and professional researchers.

Mark Musen

Biomedical informatics, Stanford

Mark A. Musen, M.D., Ph.D., is Professor of Biomedical Informatics at Stanford University, where he is Director of the Stanford Center for Biomedical Informatics Research. Dr. Musen conducts research related to intelligent systems, reusable ontologies, metadata for publication of scientific data sets, and biomedical decision support. His group developed Protégé, the world’s most widely used technology for building and managing terminologies and ontologies. He is principal investigator of the National Center for Biomedical Ontology, one of the original National Centers for Biomedical Computing created by the U.S. National Institutes of Heath (NIH). He is principal investigator of the Center for Expanded Data Annotation and Retrieval (CEDAR). CEDAR is a center of excellence supported by the NIH Big Data to Knowledge Initiative, with the goal of developing new technology to ease the authoring and management of biomedical experimental metadata. Dr. Musen chairs the Health Informatics and Modeling Topic Advisory Group for the World Health Organization’s revision of the International Classification of Diseases (ICD-11) and he directs the WHO Collaborating Center for Classification, Terminology, and Standards at Stanford University.

Cameron Neylon

Scholarly Communications, Consultant (formerly PLoS)

Cameron Neylon is a freelance researcher, consultant and is an advocate of open research practice who has always worked in interdisciplinary areas of research. He has previously been Advocacy Director at PLOS (the Public Library of Science), a Senior Scientist at the STFC Isis Neutron and Muon Facility and tenured faculty at the University of Southampton. Along his earlier work in structural biology and biophysics his research and writing focuses on the interface of web technology with science and the successful (and unsuccessful) application of generic and specially designed tools in the academic research environment. He is a co-author of the Panton Principles for Open Data in Science and the Altmetrics Manifesto, and writes regularly on the social, technical, and policy issues of open research at his blog, Science in the Open.

Karen Skinner

Pharmacology, National Institutes of Health (Retired)

Dr. Skinner retired from the National Institutes of Health in 2012, where she served as the Deputy Director for Science and Technology Development at the National Institute on Drug Abuse. Dr. Karen Skinner joined the NIH in 1989 as a program officer in Developmental Neurogenetics at the National Institute on Neurological Disorders and Stroke. She moved to the National Institute on Drug Abuse (NIDA) in 1991, and currently serves as the Deputy Director for Science and Technology Development in the Division of Neuroscience and Behavior Research at NIDA. Her current program activities at NIDA include resource discovery and sharing, informatics, computation and emerging technologies. She serves as Project Officer for the Neuroscience Information Framework, a project of the NIH Neuroscience Blueprint Initiative, and as Program Officer for the NIH Roadmap National Center for Integrative Biomedical Informatics. She also belongs to the BISTI consortium, and serves on the Trans-NIH BioMedical Informatics Coordinating Committee, and the NIH Blueprint NITRC project team.

Ben Goldacre

Medicine/Pharma,University of Oxford

Ben Michael Goldacre is a physician, academic and science writer. As of March 2015, he is a Senior Clinical Research Fellow at the Centre for Evidence-Based Medicine based at Nuffield Department of Primary Care Health Science, University of Oxford.[2] He is a founder of the AllTrials campaign to require open science practices in clinical trials. Goldacre is known in particular for his “Bad Science” column in The Guardian, which he wrote between 2003 and 2011, and is the author of three books: Bad Science (2008), a critique of irrationality and certain forms of alternative medicine; Bad Pharma (2012), an examination of the pharmaceutical industry, its publishing and marketing practices, and its relationship with the medical profession, and I Think You’ll Find It’s a Bit More Complicated Than That, a collection of his journalism. Goldacre frequently delivers free talks about bad science—he describes himself as a “nerd evangelist”.

Elba Serrano

Neuroscience, New Mexico State University

Elba Serrano’s biomedical research focuses on disorders of hearing and balance, sensory organ formation, and nanobiotechnology. Her research has been furthered by grants and awards from the National Institutes of Health, NASA, NSF, the Ford Foundation, and the Whitehall Foundation. Serrano is an advocate of interdisciplinary research and education and she collaborates with scientists and engineers at UCSD, the Center for Integrated Nanotechnologies (CINT), Harvard, MIT and NMSU. Serrano is the Principal Investigator and Program Director of NMSU’s NIH funded BP-ENDURE Building Research Achievement in Neuroscience (BRAiN) and Research Initiative for Scientific Enhancement (RISE) student training programs. She has offered courses, workshops, and lectures on science, ethics, and society for over 15 years. She is a current member of the Advisory Board to the NIH Director, the NIH NIDCD Council and the Health Sciences Advisory Council for the Hispanic Association of Colleges and Universities (HACU). Formerly, Serrano has served on the CINT User’s Advisory Board, the International Neuroethics SocietyProgram Committee, the Society for Neuroscience Professional Development Committee, and the Advisory Board for the Annual Biomedical Research Conference for Minority Students (ABRCMS).

Presentations

Hypothesis at Neuroscience Information Framework booth
Society for Neuroscience
Oct 17-21, 2015
Chicago, IL USA

Hypothesis and ORCID
ORCID Outreach meeting
Nov 3-4, 2015
San Francisco CA USA

Hypothesis: Creating a light-weight, open, portable knowledge layer over biomedicine
Webinar for Biomedical and Healthcare Data Discovery Index (bioCADDIE)
December 10, 2015

Past events

I Annotate 2017: San Francisco, California USA on 4-5 May 2017.

International Biocuration Meeting 2017: Hypothesis once again participated in the Gigascience Annotation Challenge 26-29 March, 2017 at Stanford University, California USA.

Society for Neuroscience, San Diego, California USA on Nov 12-16, 2016.

I Annotate 2016: Berlin, Germany on 19-20 May 2016.

Biocuration 2016: 10-14 April 2016 in Geneva, Switzerland. Take the Community Curation Challenge! Use Hypothesis and iClickVal to annotate as fast as you can.

FORCE2016: 17-19 April 2016 in Portland, Oregon USA and the Annotating All Knowledge Kick Off Meeting on 17 April 2016.

Who is using Hypothesis in bioscience

Hypothesis is already in use by a growing number of researchers and students in the biosciences. We are also actively looking for partners to explore the use of Hypothesis within scientific and publishing workflows, e.g., peer review, data curation, automated and semi-automated linking. If you are interested in learning how Hypothesis can help support these functions, contact us.

Attention Biocurators: Interested in controlled tagging using Hypothesis? We have developed some prototypes that allow Hypothesis to tag with controlled vocabularies and ontologies. We’d like your feedback. If interested, contact us.

Also, many in the Hypothesis community are developing tools using Hypothesis that handle more specialized use cases. See what they are up to and add your own.

Join the discussion

Hypothesis lets researchers interactively annotate current articles. Unlike commenting systems, the annotations are anchored to specific fragments of text. Hypothesis is also a great tool for Journal Clubs to annotate in public or using private groups. Here are some examples:

Data and literature curation

  • NeuroVault Database (Russ Poldrack, Stanford): A first pass Hypothesis integration into NeuroVault, a database for sharing neuroimaging data, was deployed by graduate student Vanessa Sochat to extract neuroimaging parameters from the literature.
  • Structured literature annotation (David Kennedy, U Mass Amherst): testing Hypothesis for annotating the literature to create a “Neuromorphometry report” for the NeuroImaging Tools and Resource Clearinghouse (NITRC).
  • BioStor (Rod Page, Biodiversity Institute, Glasgow): Annotation of biodiversity geo-coordinates with Google Maps

Education

Hypothesis is an excellent tool for teaching, allowing students and teachers to interact over scientific articles. We have an active program in education, led by Dr. Jeremy Dean.

  • Science in the Classroom (American Association for the Advancement of Science): Would you like to make your science more understandable? See how Hypothesis is used for annotating Science papers for educational use.

Annotate your own articles!

Did you forget a reference? Is that link broken? Do you need to add more information to a protocol or link an article to a data set? Use Hypothesis to provide updates on your published papers.