Archive for the ‘Data Spotlight’ Category

Introducing the Aging Portal

Posted on October 8th, 2014 in Anita Bandrowski, Data Spotlight | No Comments »

The Neuroscience Information Framework, has been asked many times “how can we sort through this dizzying amount of data?” to which we have never had a great answer until now. With SciCrunch, a shared portal infrastructure that allows users to create their own portals into subsets of data, NIF has created a dedicated subset of resources funded by and of interest to the aging research community.

The portal can be found here: http://scicrunch.com/Aging

 

The NIA funded a small award to pull interesting resources out of the main, at times overwhelming quantity, of NIF resources into their own portal, and we have done this for 14 databases including the following that were brought in specifically for the portal:

Aging Genes and Interventions Database

AnAge

Human Mortality Database

Lifespan Observation Database

 

Other resources that were already present in the Data Federation such as Aging Genes Database and Clinical Trials. However, we hypothesize that with many databases only subsets of the data are relevant to aging, for example our integrated Clinical Trials data are relevant to aging when the population is aged. Similarly Gene Ontology Annotations for aging-related genes are included. If this is not a valid assumption, we would love to hear from you.

We hope that this portal is a useful tool for aging researchers, who can start looking for aging relevant data or databases funded by the NIA by looking at the subset of community databases and hopefully recover reasonable subsets of data. However, if the subset of data is not sufficient for the purposes of the researcher, all of the other databases aggregated by NIF are available and accessible via a fully configured search interface under the “more resources” tab.

 

Happy Data Hunting!

NIF now pleased to serve more electrophysiology data

Posted on September 30th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | 1 Comment »

For years, physiology has been lagging far behind anatomy as data sharing is still in infancy in that community as opposed to being fairly standard now in neuro-anatomy.

We are pleased to announce that the Physiobank registry resource from MIT, containing data from a set of physiology experiments has been added to the NIF Data Federation.

 

This brings us to 6 sources of data (anatomy is still winning, but perhaps we can change that)

CRCNS, a repository of e-phys data (patch clamp mostly)

NeuroElectro, a rather large listing of cellular properties mined from e-phys papers

NeuronDB, a curated set of e-phys properties of known cell types including currents, receptors and transmitters

EEG-base, a repository of EEG data

Neurodatabase, a repository of extracellular data sets.

 

Note, this list may be incomplete because it does not include Model data, so please see Integrated Models, a virtual database currently indexing computational models from:ModelDBOpen Source BrainSimTK and  CellML.

 

New in NIF! Find your MRI images in NeuroVault

Posted on September 29th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

New to NIF this week is NeuroVault.

NeuroVault is a public repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies. Many of the data are also accessible from OpenfMRI.

There are currently 369 images, and we anticipate many more in the coming months.

If you wish to share your data via NeuroVault click here.

Neurodata Without Borders needs your imput!

Posted on August 12th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Dear Colleague,

The Neurodata Without Borders (NWB) project has just started. The project goal is to build a common data format for neurophysiology data from Allen Brain Institute, Janelia Farms and two labs from NYU and Caltech.  Although focusing on a limited set of use cases, the project also aims to develop products that will serve the broader community.

At this point we would like to solicit community input about ideas/approaches for designing a generalizable neurophysiology data format. If you are interested in contributing to this project, please review the project description at:
https://crcns.org/NWB
and fill out the questionnaire:
https://docs.google.com/forms/d/1CNTd4M-8kQ_WhEZc7n7WxpTa0LOupt_q3z21E1fRxjM/viewform

On the basis of the questionnaire responses and ensuing communication, we will organize the first hackathon meeting of the project, to be held November 20 – 22, 2014 (just after SfN) at Janelia Farm, in Ashburn, Virginia.  At this hackathon we will discuss in detail the requirements for a common format based on the project use cases and also discuss, compare and evaluate alternative techniques for implementing the common format.

More information about the project is available in a recent press release: http://www.kavlifoundation.org/kavli-news/prominent-us-research-institutions-announce-collaboration-toward-sharing-and

Please forward this email to anyone you know with relevant expertise who may be interested in contributing to this project.

Thank you,
Fritz Sommer and Jeff Teeters
Redwood Center for Theoretical Neuroscience
UC Berkeley

Scientific Data Reproducibility, a conversation – July 23, 2014, 1 pm EST

Posted on July 16th, 2014 in Anita Bandrowski, Author, Data Spotlight, Webinar Announcement | 2 Comments »

Drs. Martone of NIF and Iorns of Science Exchange among others address important issues around reproducibility of data.

A video recording of this event is available here. Note you have to register to see it.

Title: Improving Scientific Reproducibility In The Life Sciences: Considerations for Researchers, Publishers and Life Science Tool Providers
Date: July 23, 2014     * completed * video available  
Time: 1:00 PM Eastern (10:00 AM Pacific)         
Duration: 90-minutes

In recent years scientific reproducibility has been a topic of much debate.  This debate has been sparked in part by the now infamous “Amgen Study” conducted by Glenn Begley and team that found fewer than 7 of 53 landmark pre-clinical studies published between 2002 and 2012 could be reproduced as described in the initial publication.

The factors that contribute to poor reproducibility in pre-clinical research are complex; some relate to systemic problems in how research is conducted and funded while others relate to how research is documented and published. Recently the role that scientific suppliers, publishers and researchers can play in improving research reproducibility has come into sharp focus. Improving reagent traceability and documentation in literature have been identified as areas that can make a significant contribution to increased reproducibility.

This webinar will bring together thought leaders that are behind some of these efforts and explore how their projects are contributing to the goal of improving scientific reproducibility.


Have you ever wondered what is the longest gestation period for a bird, or what is the maximum age for a squirrel?

Posted on July 15th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Well wonder no more! NIF is here to help answer these burning questions.

This week we have a couple of new sources from the aging community: AnAge and the Lifespan Observations Database.

The AnAge data set contains data based on the phylogenetic tree and users can select or search for individual species or groups of organisms from kingdom or phylum to class like rodents or birds.

Screen Shot 2014-07-15 at 10.13.14 AM

I have often wondered which rodent reaches female sexual maturity latest. Finally my curiosity is satisfied!

Screen Shot 2014-07-15 at 10.14.32 AM

 

Can you find the answer to the question: What is the largest rodent?

Let us know what you have wondered about that can now be answered using this data.

 

NITRC can host your data!

Posted on May 15th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Dear NIF community;

Many of you are aware of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC – nitrc.org) for finding and hosting software. What is somewhat less well known is that NITRC can host your data for public sharing as well. As part of NITRC’s three broad classes of functionality (resource hosting; image repository; and virtualized computational environments) broad support for data sharing is provided. Use NITRC data sharing to satisfy your funders and publishers data sharing requirements.  Contact the Moderator at moderator@nitrc.org for detailed information and assistance.

Thank you.
-The NITRC Management Team

The ABA and Gensat expression data has been substantially compared and it does not match up all that well

Posted on January 21st, 2014 in Anita Bandrowski, Data Spotlight | No Comments »

An article by Zaldivar and Krichmar discusses a comparison and alignment of data (never an easy thing) between the Allen Mouse Brain Atlas and Gensat data, mainly. This article deals with the issue of data alignment and a real look at the two resources, gathering data from different sources with ABA a high throughput technique and Gensat was largely used for the myriad of ISH studies they had gathered.

The two sources are eerily different, see table 2 below.
429_2012_473_Tab2_HTML
Note, green means alignment, blue and red seem to dominate though!

My question when looking at something like this is how much overlap should we expect?
If there is not much overlap, then what conclusions should we make based on any one gene expression study?

By the way, the authors used the Neuroscience Information Framework to search gensat, but you can do your own comparison because NIF has an “integrated view” giving a quick overview of the data from Gensat, MGI and ABA.

Vasculature Morphogenesis: Synopsis of three related articles by Halina Witkiewicz, Phil Oh and Jan Schnitzer

Posted on January 3rd, 2014 in Data Spotlight, Essays, General information | No Comments »

The following is is a guest blog by Krystyna Gutowska.
The topic is a set of three articles by Witkiewicz et al. previously blogged about by NIF as an exemplar of open access publishing and a new open review process utilized by the Faculty of 1000 journals.

Common sense dictates that inhibiting malignant tumor growth (cancer) should be possible by inhibiting formation of new blood vessels. An artistic vision of that belief was painted in 1940 by Diego Rivera “The Hands of Dr Moore” (San Diego Museum of Art in San Diego). In 1972 Judah Folkman presented the concept for therapy of solid tumors by the anti-agiogenesis treatment [Greek angeion = vessel] for which he became well known. Yet, the quest for such treatment has not resulted in finding the cure for cancer, so far.

Screen Shot 2014-01-06 at 9.32.10 AM

In countless review articles the formation of tumor vessels was presented graphically to reflect researcher’s current understanding of how it was supposed to happen at the cellular and molecular level. Instead of such artistic and graphic representations, the three studies published in F1000Research on January 10th 2013 provide photographic documentation of the process that turned out to be different from previously imagined. Nobody had expected blood elements to be produced at the site of new tissue growth first and subsequently single cells to assemble around them into vessels. That would have been counter-intuitive; after all, to handle any fluid one needs a vessel. Besides, the blood formation after birth was supposed to be localized in bone marrow (medulla ossea), not extramedullary. Therefore the new vessels were assumed to be formed first and filled with blood next. That misconception prevailed in science for a long time. The essential contributing factor was the false belief on how the red blood elements were formed. Specifically, how the erythrocyte precursors (erythroblasts) were eliminating their nuclei to become anucleated erythrocytes, meaning: red cells without nucleus.

Paradoxically, the concept of the nucleus being separated from cytoplasm by expulsion (resembling separation of egg yolk from the white) came from 1967 morphological studies that used electron microscopy, just like the 2013 studies discussed here. Although the same methodology was used at both times, the animal models subjected to the ultrastructural analysis were different. The critical difference was the type of analyzed tissue (bone marrow or spleen versus tumor). In the bone marrow and spleen the erythrogenesis is relatively rare and to observe it the process had to be experimentally stimulated by inducing anemia in dogs or mice. However, the tumor-hosting mice used recently were not subjected to any pathogenic treatment except the surgical implantation of cultured tumor cells into dorsal skin fold of the animals. In that model the erythrogenesis was spontaneous and frequent enough for capturing images of various stages. The expulsion of the nucleus from the erythroblasts was not happening and macrophages (the cells said to internalize and digest the released nuclei) were rare in that environment. The nuclei were degraded in the process of erythrogenic autophagy not by the macrophages but by the very cells they were a part of. Each erythrogenic cell was remodeled into a few smaller red vacuoles by a nucleo-cytoplasmic conversion. No nuclear waste was released for macrophages to clean up. Such red vacuoles are no longer cells, although they have been referred to as the erythrocytes (red cells). The 2013 studies use the term erythrosome (red body) as a synonym for erythrocyte because it describes the sub-cellular nature of those blood elements better. The cells converting into erythrosomes were visually recognizable in tissue sections and their location outside bone marrow was evident.

The erythrogenesis turned out to be the central element of the vasculature formation induced locally by the growing tumor or by healing of the surgical injury inflicted by the implantation of the tumor cells; figuratively speaking and literally, i.e., as a source of energy and as a structural morphogenetic element chemotacticly attracting cells. (Erythrocytes are known to secrete high energy molecules, ATP). Those ultrastructural studies demonstrated for the first time that the extramedullar hematopoiesis and vasculogenesis were inseparable in live animals; hence, the term ‘vasculature’ included blood and vessels. Historically, the term ‘angiogenesis’ (expansion of existing vessels) was replaced by ‘neovasculogenesis’ (generation of new vessels from bone marrow derived precursor cells). Now, the most appropriate term appears to be ‘vasculature morphogenesis’ (formation of blood and vessels from local tissue stem cells).

In the first article the authors discuss the implications of the new findings for malignant as well as non-malignant tissue or organ morphogenesis (the organoblasts concept) and for tissue definition. The second article shows formation of a capsular vasomimicry that could potentially lead to spreading of tumor cells to various locations by fusing with morphologically similar lymphatic vessels or veins, i.e. to metastasis. The third article deals with tumor energy metabolism and explains the over half a century old Otto Warburg’s conjecture by cellular heterogeneity of tumors. That connection was missed by metabolic studies based on samples isolated from tissues because the isolation process destroys the tissue. Also missed was the role for the anaerobic metabolic pathway discovered by Warburg during cell division, when the structural changes in the mitochondria indicate their temporary functional disability. That reversible malfunction correlates with a particular stage of the cell cycle (mitosis).

The 1967 conclusion on the mechanism of the erythrocytic enucleation by expulsion of the nucleus derived form pathologically changed systems was erroneously extrapolated to systems not modified experimentally. Consequently it had a long-lasting and misleading effect on multiple studies in vascular biology. The appealing concept of inhibiting angiogenesis to stop tumor growth suffered from lack of understanding the cellular interactions leading to the vasculature formation (blood as well as vessels). To study those interactions the tissue must be preserved. Electron microscopy supported by immunocytochemistry (using antibodies to identify specific molecules in situ) is the method of choice for such purpose. The observations reported in the three articles discussed here appear of profound significance for tissue morphogenesis in general, not only in malignancy.

Refocusing on inhibiting tumor vasculature formation, with the full force of currently available technologies, presents a realistic chance to cure solid tumors in large number of patients despite the tumors’ genetic diversity perpetually introduced during cell divisions. Such strategy would not interfere with proliferation of normal cells that does not result in tissue growth. One prominent example is renewal of the gut epithelium. From clinical point of view the gut epithelium is critically important because of the role it plays in absorption of nutrients.

Congratulations to Phil Bourne, the New NIH Director for Data Science!

Posted on December 10th, 2013 in Anita Bandrowski, Data Spotlight, Force11 | No Comments »

U.S. Department of Health and Human Services NATIONAL INSTITUTES OF HEALTH NIH News Office of the Director (OD) <http://www.nih.gov/icd/od/> For Immediate Release: Monday, December 9, 2013

CONTACT: NIH Office of Communications, 301-496-5787, <e-mail:nihnmb@mail.nih.gov>

NIH NAMES DR. PHILIP E. BOURNE FIRST ASSOCIATE DIRECTOR FOR DATA SCIENCE

National Institutes of Health Director Francis S. Collins, M.D., Ph.D, announced today the selection of Philip E. Bourne, Ph.D., as the first permanent Associate Director for Data Science (ADDS).  Dr. Bourne is expected to join the NIH in early 2014.

“Phil will lead an NIH-wide priority initiative to take better advantage of the exponential growth of biomedical research datasets, which is an area of critical importance to biomedical research.  The era of ‘Big Data’ has arrived, and it is vital that the NIH play a major role in coordinating access to and analysis of  many different data types that make up this revolution in biological information,” said Collins.

Dr. Bourne comes to the NIH from the University of California San Diego, where he is the Associate Vice Chancellor for Innovation and Industry Alliances of the Office of Research Affairs and a Professor in the Department of Pharmacology and the Skaggs School of Pharmacy and Pharmaceutical Sciences.  He also is the Associate Director of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank.  Dr. Bourne was trained as a physical chemist and obtained his Ph.D. from The Flinders University in South Australia.

Dr. Bourne’s professional interests focus on relevant biological and educational outcomes derived from computation and scholarly communication.  This work involves the use of algorithms, text mining, machine learning, metalanguages, biological databases, and visualization applied to problems in systems pharmacology, evolution, cell signaling, apoptosis, immunology, and scientific dissemination.  He has published over 300 papers and five books.  One area to which he is extremely committed is to furthering the free dissemination of science through new models of publishing and better integration and subsequent dissemination of data and results.

Collins added, “I also must recognize and thank Dr. Eric Green, who served as the Acting ADDS since I announced the search to fill this new position.  His willingness to take on this challenging role in its inception, and to get the ball rolling on the enormous tasks that accompany this high-priority initiative, is sincerely appreciated.  Eric is certain to remain a tremendous source of knowledge and support as Phil continues the NIH’s effort to manage ‘Big Data’.”

About the National Institutes of Health (NIH): NIH, the nation’s medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit <www.nih.gov>.

NIH…Turning Discovery into Health — Registered, U.S. Patent and Trademark Office ###

This NIH News Release is available online at:

<http://www.nih.gov/news/health/dec2013/od-09.htm>.