Here are the top 25 accessed databases at NIF for January 2012:

1. Grants.gov/Opportunity
2. CCDB/All Information
3. SumsDB/Activation Foci
4. ResearchCrossroads/Grants
5. AntibodyRegistry/ABs
6. GENSAT/GENSAT
7. Drug Related Gene Database/DRG
8. BrainInfo/Brain Region
9. OneMind/BioBanks
10. RePORTER/CurrentNIHGrants
11. DrugBank/Drugs
12. ClinicalTrials/ClinTr
13. NIF Integrated Nervous System/Connectivity
14. NIF Integrated Video/Videos
15. ModelDB/Models
16. HumanBrainAtlas/Michigan
17. NIF Integrated Animals/Available
18. OMIM/Genes
19. NIHNeuro/Microarray Consortium
20. AllenInstitute/MouseBrainAtlas
21. NIF Integrated Software/Info
22. BrainMaps/Atlas
23. Gemma/Microarray
24. WikiPathways/ChemPathway
25. GeneNetwork/Info

We are pleased to announce the release of NIF v4.0, which went live during the week of December 5th, 2011. NIF v4.0 has a number of features that improve overall performance of the Neuroscience Information Framework, as well as user focused features to improve navigation in the search results.

On the backend, we now have Solr serving our Lucene indices. With Solr, we can access advanced search functionality while processing queries to NIF. Also, our system has been upgraded to solid-state drives (SSD) to improve retrieval performance.

For the end-user, there have been a few features that are highlighted with the release of NIF v4.0 that we would like to expand on. Many users familiar with NIF know that we have a mountain of neuroscience-related data  – some 336 million records. While searching for data, users often are looking for a smaller subset than a simple search result can provide. To achieve this, users are now able to “Filter” on each column within the Data Federation. The filtering functionality limits the search result set to records containing the filtered string. For example, in the NIF Integrated Animals view, results are retrieved across the Rat Genome Database (RGD), International Mouse Strain Resource (IMSR), Caenorhabditis Genetic Center (CGC), and Zebrafish International Resouce Center (ZIRC). If a researcher is only looking for potential zebrafish animal models, they are now able to use “zebrafish” as a filter on the “Organism” column. A video tutorial for the Filtering feature is available at NIF 4.0 – Advanced Search Filtering Functions.

NIF users also desired a way to save search results or at least a snapshot of them while they try out different searches. One way to achieve this, is to “Load in a new window”, which is available on all data sources in NIF v4.0. Clicking this button will, as it suggests, loads the current result set into a new window useful for data comparisons. Additionally, users are able to use the “Export” feature, which is not new to NIF v4.0, but permits more through massaging of search results using popular spreadsheet or data analysis software. Lastly, the “View in Pivot” option desires some mention. Pivot is an exploratory interface available for most Image data type resources. This interface allows users to dynamically organize and sort images into various categories provided by the resource.  A video tutorial highlighting each of these features is available at NIF 4.0 – Advanced Search Results Features – New Window, Pivot and Export.

Lastly, NIF Literature has received some noteworthy improvements. The literature indices, gathered from PubMed and PubMed Central (open-access), have been collapsed into a single tab with the release of NIF v4.0. Additionally, we have provided “facets” for the user. Facets are produced from the top result count across Year, Authors and Journals. This way, users are able to quickly reduce search results to a particular area of interest, as well as gather a quick overview of the top authors or journals related to their search string. A video tutorial highlighting these features is available at NIF 4.0 – Scientific Literature Search & Faceting

If you have any questions or comments please feel free to visit the NIF Forum to post and become engaged in the discussion!

What are people looking for at NIF?  As the year draws to a close, we bring you the NIF Top 10.

The NIF Top 10 Categories for December 2011 are….

1. Nervous System Level:Multi-Level
2. Nervous System Level:Brain Regions
3. literature
4. Data Type:Images
5. Data Type:Antibodies
6. Data Type:Animals
7. registry
8. Data Type:Drugs
9. Data Type:Connectivity
10. Data Type:Disease

As the year ends, we begin a new series of posts, the NIF Top 10.

Here are the Top 10 Searches at NIF for December 2011

1. cerebellum
2. “Purkinje Cell”
3. “Diencephalon”
4. antibodyregistry
5. hippocampus
6. “Brainstem”
7. s100b
8. sert
9. “Frontal Lobe”
10. “Oligodendrocyte Precursor Cell”

NIF Webinar – June 21st, 2011

“Ontology-based Analysis of Human Brain Activity; Recent work in the Development & Application of NEMO” was presented by Dr. Gwen Frishkoff, the Director of the NEMO consortium.

The goal of the NEMO project is to represent what we know about complex patterns in human event-related potentials. As discussed by Dr. Frishkoff, most neuroscientists and electrophysiologists can agree that there are 3 primary categories to analyze patterns in EEG and MEG data: Time, as the latency of peak positive or peak negative potentials, Space, as in scalp topography and function, the experimental context in which patterns are observed (i.e. presentation of visual stimulus).

The major problem in EEG and MEG data analysis, according to Dr. Fishkoff, is a lack of integration.  The NEMO project has a three tiered approach to this problem;

1) Develop a formal ontology for ERP domain concepts.
2) Create a suite of tools for automated-pattern extraction and ontology-based annotation for better data analysis.
3) Apply tools across datasets to prove applicability.

For more information, we invite you to view the full webinar here.

As we push forward integrating neuroscience resources, literature & data – we are always looking for novel, helpful and exciting neuroscience related content to integrate within the semantically-enhanced NIF system. In fact, if you have a neuroscience resource and would like to register it with NIF, please check out the tutorial for Registering your Resource with NIF.

Scientists, students, administrators..practically everyone is reading multiple large documents per day which requires time, attention and, of course, enough lexical knowledge to fully grasp its meaning. Fortunately, there is YouTube for that downtime (i.e. the latest cat meme). However, there have been a number of new sites dedicated solely to scientific content.

Scivee.tv is a great example.

They allow scientists to upload video summaries of their work – so rather than just read the article, you are able to watch the scientist explain the research and even watch the video with an auto scrolling feature taking you to the relevant part in the article – check out the video here.

the Journal of Visualized Experiments (JOVE) is another great example.

With a special section dedicated to neuroscience, JOVE provide excellent video tutorials for laboratory protocols and methods – one thing, in particular, that is easier to pick up by watching rather than reading.

Lastly, YouTube does in fact have a lot of interesting, neuroscience-related videos – most of them being video presentations from conference proceedings or well-produced interviews with prominent scientists.

In the future, we would like to curate these videos and provide the NIF community to search for and save their favorite neuroscience videos. We will be sure to update the community as these features roll out and as always we love to hear your feedback. If you have any ideas or know of similar science-related video sites, please feel free to contact us by any means or post a comment below!

Inside NIF appears every Wednesday on the NIF Blog. Join us each Wednesday to learn more about what’s happening at NIF, your Neuroscience Information Framework.

After the success of Inside NIF: The Cell: An Image Library – mobile phone wallpapers, we have decided once again to comb The Cell: An Image Library for exciting and interesting neuroscience images for your enjoyment and download – this time as desktop wallpapers. To load the full-size image, simply click the image you like.

Check back on the first Wednesday of each month for new neuroscience images gathered from Image sources within the Neuroscience Information Framework!

Image 1: Filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons.

(Authors: Dieter Brandner, Ginger Withers )

Image 2: Interneurons expressing EGFP from the 5HT3 receptor promoter in the dorsal hippocampus colabelled for the CB1 cannabinoid receptor (red) and counterstained with DAPI (blue) to show the cell layers.

(Author: Margaret I. Davis)

Image 3: Hippocampal neurons expressing EGFP from the Nr4a1/Nur77 promoter colabelled with calbindin 28K (red) and stained with DAPI (blue) to show cell layers.

(Author: Margaret I. Davis)

Image 4: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter colabelled for the CB1 cannabinoid receptor in hippocampal CA1.

(Author: Margaret I. Davis)

Image 5: The CA region of the hippocampus of adult rat, immunostained to reveal dendrites of neurons (red), astroglia (green) and all nuclei (blue).

(Authors: Christopher Wallace, Ginger Withers, Tony Cooke )

Inside NIF appears every Wednesday on the NIF Blog. Join us each Wednesday to learn more about what’s happening at NIF, your Neuroscience Information Framework.

I recently came across an interesting blog post titled “Is Academia Eating Its Young“, written by Bill Benzon. The main focus revolves around blogging in the academic community, particularly that there is no professional credit to be gained from blogging and many times can be viewed as detrimental to one’s career.

Upon this realization, Bill suggests that “it’s pointless to try and legitimate blogging in the current academic world.” Granted, I can understand Bill’s perspective and empathize with the nature of contemporary academia – at the Neuroscience Information Framework, we are investigating ways to harness the intellectual creativity that emerges from blog posts and other social media.

There are thousands of scientist bloggers, and a number of sites, such as F1000, The Third Reviewer and AkaWiki, which are dedicated entirely to discussion of recently published scientific articles. Often the personal and colloquial nature of blogs allows for pertinent praise and/or criticisms to come through in a way that is typically found in the closed doors of a journal club. Moreover, these posts are frequently very helpful to someone new in a particular field or someone trying to quickly extract the main points of an article.

At NIF, we are currently trying to aggregate the “social buzz” that surrounds popular neuroscience articles in order to harness the intellectual value contained therein. We envision that one day, while using NIF to find the latest data, literature or grants around a particular subject you will be able to quickly access and review blog posts, tweets and comments surrounding these objects from a single portal. In this way, albeit indirectly, professional credit could possibly be gleaned from the online activity of scientists. Moreover, communities of like minded scientists could be formed and active scientific discussions could take place.

We look forward to implementing some of this functionality with the release of NIF 4.0, but would like to gather thoughts, comments and ideas from the community. Would you find the “social buzz” of an article interesting or valuable? What would you like to do with this information? How can we deliver it most effectively? As always, we appreciate any feedback!

The Cell: An Image Library™ is a open, easy to use repository of high-quality images, videos and animations of cells. Given their efforts to semantically annotate uploaded images, non-scientist users can quickly browse to a particular type of cell, or cellular process with ease.

NIF recently hosted a webinar with David Orloff, manager of CIL, who gave an excellent overview of their philosophy, technologies and future directions. It also inspired the NIF team to browse around in CIL, bringing to you some of the best neuroscience related images we could find – formatted in iPhone wallpaper size. Check them out below:

Image 1: Cultured hippocampal neurons, immunostained for MAP2 & PSD95

(Author: Dieter Brandner & Ginger Withers, Whitman College )

Image 2: Labeled mitochondria in fibroblasts.

Image 3: Mouse Ovary with tublin labeled – NOT a planet!

Image 4: Surface of epidermal cell

(Authors: Don W. Fawcett & Wolf Fahrenbach)

Image 5: Somatic basal bodies at cytoproct ridge

Finding a working antibody for your proteins of interest can be a difficult process. Similar antibodies are available from a number of different antibody providers and depending on which vendor your order the antibody from, you could have varying levels of success. The Neuroscience Information Framework currently maintains two antibody resources: the Antibody Registry and the Antibody Table.

The Antibody Registry serves the scientific community by providing a list of antibodies (> 890,000) as well as a set of unique identifiers for commercial and non-commercial  antibody reagents. These features enhance scientist’s ability to keep track of data generated using a specific antibody. In other words, it allows antibody providers to determine which experiments used a particular antibody and it allows scientists to track usage of antibodies developed within their lab.

The Antibody Table is a compilation of data submitted from most antibody vendors, such as Labome and Biocompare.

Searching for NIF for antibodies can be done using the following search syntax: antibodyregistry gene:grm1 (shown below).

This will limit your results to within the Antibody Registry and provide you with product information organized by genes, species, and reagent types (antibodies, recombinant, proteins, ELISA, siRNA, cDNA clones). From here, you should be able to locate an antibody useful for your particular experiment design, see how it has worked for other experiments and click out to an ordering page to get the research moving forward!

NIF is always working to increase the number of antibody resources and we invite you to recommend a resource. Additionally, the Antibody Registry allows any user to submit a new antibody or set of antibodies via web form or spread sheet upload.

For more information on the Antibody Registry, please check out the Antibody Registry tutorial.