Hello,
NIF 4.1 has been released, as of March 21, 2012. We hope you find the new features helpful as we continue to improve upon and expand our efforts. You may find release notes on the site.
As with any new release, technical difficulties are possible. If you experience any difficulties at all, please contact us to let us know.
Thank you.
Here are the top 25 searches in NIF for March 2012:
Here are the top 25 accessed databases for March 2012:
Here are the top 25 accessed databases in NIF for February 2012.
Here are the top 25 searches in NIF for February 2012.
The Representation of Gender in NIF’s Data Holdings – Click the link to go to the full PDF document, which includes at the end an interactive chart.
The following is excerpted from the full document. In addition, there is an explanation of the interactive chart, which is included at the end of the PDF.
The Neuroscience Information framework indexes 150 individual databases deeply, meaning that it exposes data from those databases and data sets. These include large aggregators of data such as the model organism databases (mouse genome informatics, MGI) and small data sets such as the 1,000 functional connectomes. These holdings break down to approximately 350 million individual data records, most of which are tagged and aligned to some extent to a structured vocabulary.
In the first pass, the term male was searched exclusively. Of the 350 million total records in NIF’s holdings, the search for male reveals that there are 159 million records that mention the term male as well as 5.9 million articles: http://neuinfo.org/nif/nifgwt.html?query=male
Searching female exclusively reveals that 127 million records and 5.9 million articles mention the term female: http://neuinfo.org/nif/nifgwt.html?query=female
In order to break down some of these findings, we can examine both the literature and the data results and compare the prevalence of male versus female. All raw data and numbers are available in the attached appendix.
. . .
The interactive chart is Figure 8: Heat map of directed search queries into NIF’s data holdings broken down by source and query. Each box contains the number of results for each search executed in NIF; these numbers were used to construct the figures above. For a fully interactive heat map please see the attached excel sheet. Clicking on the column names should lead to a general search of the NIF data; each row header is labeled with a database name and links to a descriptive page about that database. Clicking on all green cells should execute a search against a specific database.
Go to the full PDF document to access the interactive chart.
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….
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
