Green digitization: Botanical collections data answer real-world questions | EurekAlert! Science News

“Special issue of Applications in Plant Sciences explores new developments and applications of digital plant data

Even as botany has moved firmly into the era of “big data,” some of the most valuable botanical information remains inaccessible for computational analysis, locked in physical form in the orderly stacks of herbaria and museums. Herbarium specimens are plant samples collected from the field that are dried and stored with labels describing species, date and location of collection, along with various other information including habitat descriptions. The detailed historical record these specimens keep of species occurrence, morphology, and even DNA provides an unparalleled data source to address a variety of morphological, ecological, phenological, and taxonomic questions. Now efforts are underway to digitize these data, and make them easily accessible for analysis. Two symposia were convened to discuss the possibilities and promise of digitizing these data–at the Botanical Society of America’s 2017 annual meeting in Fort Worth, Texas, and again at the XIX International Botanical Congress in Shenzhen, China. The proceedings of those symposia have been published as a special issue of Applications in Plant Sciences; the articles discuss a range of methods and remaining challenges for extracting data from botanical collections, as well as applications for collections data once digitized. Many of the authors contributing to the issue are involved in iDigBio (Integrated Digitized Biocollections), a new “national coordinating center for the facilitation and mobilization of biodiversity specimen data,” as described by Dr. Gil Nelson, a botanist at Florida State University and coeditor of this issue….”

Welcome to Cogprints – Cogprints

“Welcome to CogPrints, an electronic archive for self-archive papers in any area of Psychology, Neuroscience, and Linguistics, and many areas of Computer Science (e.g., artificial intelligence, robotics, vison, learning, speech, neural networks), Philosophy (e.g., mind, language, knowledge, science, logic), Biology (e.g., ethology, behavioral ecology, sociobiology, behaviour genetics, evolutionary theory), Medicine (e.g., Psychiatry, Neurology, human genetics, Imaging), Anthropology (e.g., primatology, cognitive ethnology, archeology, paleontology), as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition….”

bioRxiv.org – the preprint server for Biology

“bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals….”

ImmPort Home

“ImmPort is funded by the NIH, NIAID and DAIT in support of the NIH mission to share data with the public. Data shared through ImmPort has been provided by NIH-funded programs, other research organizations and individual scientists ensuring these discoveries will be the foundation of future research….

The Immunology Database and Analysis Portal (ImmPort) has been developed under the ImmPort Contract by the Northrop Grumman Information Technology Health Solutions team for the National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID), Division of Allergy, Immunology, and Transplantation (DAIT).

ImmPort is a partnership between researchers at the University of California-San Francisco, Stanford University, the University of Buffalo, the Technion – Israel Institute of Technology, and Northrop Grumman.

The goals of the ImmPort project are to:

  • Provide an open access platform for research data sharing
  • Create an integrated environment that broadens the usefulness of scientific data and advances hypothesis-driven and hypothesis-generating research
  • Accelerate scientific discovery while extending the value of scientific data in all areas of immunological research
  • Promote rapid availability of important findings, making new discoveries available to the research community for further analysis and interpretation
  • Provide analysis tools to advance research in basic and clinical immunology…

Private data and pre-release data are stored in private workspaces of investigators at the ImmPort site located at NIAID….”

Extracting research evidence from publications | EMBL-EBI Train online

“Extracting research evidence from publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation.

This webinar took place on 5 March 2018 and is for wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically. Some prior knowledge of programmatic access and common programming languages is recommended.

The webinar covers: Available data (annotation types and sources) (1:50) API operations and parameters and web service outputs (8:08) Use case examples (16:56) How to get help (24:16)

You can download the slides from this webinar here. You can learn more about Europe PMC in our Europe PMC: Quick tour and our previous webinar Europe PMC, programmatically.

For documentation, help and support visit the Europe PMC help pages or download the developer friendly web service guide. For web service related question you can get in touch via the Google group or contact the helpdesk [at] europepmc.org”>help desk.”