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”

The goal of the AntibodyRegistry is to provide a stable, traceable, permanent identifier to all antibody products created by large commercial vendors and individual labs that can be included in any publication as a way to easily identify the antibody used in any scientific paper and trace that antibody back to the creator.

Within the Neuroscience Information Framework, the AntibodyRegistry provides results on antibody IDs, Antibody Name, Antibody Target, Target Species, Vendor, Clonality, Clone ID, Source Organism, Comments and Articles in which the particular antibody was used.  Whats more, the Antibody Registry is a deeply integrated, ‘virtual’ database pulling information from BioCompare, swant, the Journal of Comparative Neurology’s Antibody Database, Labome, NeuroMab and Novus within a single, unified results view.

Therefore, your search for a particular antibody no longer requires visiting multiple website (each with a slightly different lexicon) if you utilize the semantically enhanced search at NIF. For an example, check out the tutorial below.

Beginning from NIF’s homepage (neuinfo.org); we can search for “gene:pfdn2″. The search will return all the attributes mentioned above.

Clicking on the antibody ID will take you to the Antibody Registry website with more detailed information that looks like following.

Clicking on the Antibody name from the search result will take you to individual database that holds the information about the antibody.

For more detailed instructions on how to use Antibody Registry, please visit the tutorial.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

Gene Expression Omnibus (GEO) is an another database of NCBI that holds gene expression information. It international public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomics data submitted by the research community. It provides robust and versatile database of gene expression profiles that provides an opportunity for scientists to easily submit their research and query for others’ works.

NIF’s federated search engine provides variety of information from GEO, including GEO Accession, experiment description, experiment type, organism, platform, technology and contributor. Any of these categories can be used to search related expression profiles in GEO. For example, if we wanted to look up some data on human’s snp variation. We can search for “human snp variation” and navigate to Data Type > Microarray > GEO:GEO, and browse for any gene expression profile of interest (shown below).

Clicking on the GEO accession number will direct the users to the more detailed page in GEO. The page will show you more detailed description of the experiment and its results. They also have downloadable files that users can download.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

Last week, we had a look at PubMedHealth: Drug but this was just scratching the surface of this resourse. PubMedHealth holds a wide spectrum of  information to aid scientists in research. In this blog, we will explore PubMedHealth: Test, a portion of PubMedHealth that focuses on tests and treatments.

In NIF, you can find description of biomedical tests as well as information which will help understand test results. For example, if we wanted to learn more about PET scans, we search for it in the NIF with search syntax “PET scan”. The result returns test name, test description, title (which is a question regarding the test), and text (which is an answer to the question). The result also shows different kinds of PET scans (shown below).

You can click on the test that you are most interested in, and NIF will take you to the PubMedHealth website for more information.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

In previous blog post, we have looked at NCBI’s Entrez: Gene. This week we will be take a look at another component of NCBI, PubMedHealth: Drug. PubMed Health offers up-to-date information on diseases, conditions, drugs, treatment options, and healthy living, with a special focus on comparative effectiveness research from institutions around the world. We will be focusing on the drug portion and how it can be accessed through the NIF.

Drug title, questions regarding the drug and its answers can be searched through the NIF. For example, if you need more information on oxycodone, a strong pain reliever, try searching NIF for “oxycodone use”. PubMedHealth: Drug can be navigated by Data Type > Drugs > PubMedHealth: Drug (shown below).

The results will show the drug name, title (which is a question), and text (which is an answer to the question). Clicking the drug title will take you to the PubMed Health page with more detailed information about the drug.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

The National Center for Biotechnology Information (NCBI) is a national institute under the National Library of Medicine which holds vast amounts of biological data. Entrez is an web portal or federated search engine provided by NCBI to allow scientists to access this information. In this blog post, we will look at NCBI Entrez:Gene, one of the many databases in the Entrez system.

Information in NCBI Entrez: Gene can be easily accessed through NIF by searching for specific gene of  interest. For example,  to learn more about the gene pca, try performing the following search in NIF: “gene: pca”. NCBI Entrez:Gene can be found under Nervous System Level > Gene > EntrezGene: NCBIGene (shown below).

The result displays the Gene Symbol, Synonyms, Type, Description and Organism. Clicking on the gene name will take you to the NCBI Entrez:gene portal with more details about the gene.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

The Cell: An Image Library is a public and easily accessible resource database of images, videos, and animations of cells. It captures a wide range of organisms, cell types, and cellular processes in order to advance research on cellular activity and ultimately improve human health.

Through NIF, The Cell Image Library can be searched by a specific cell, brain region or biological process. For example, a search for an image of the tectum returns results found under Data Type > Images > CellImageLibrary (shown below) or Nervous System Level > Cellular Level > CellImageLibrary.

Here you can find the image file name, subject type, attribution, image description, cellular component and biological process. Clicking on the image will take you to the library’s website (shown below).

So go ahead a give it a try, search NIF for a biological process – synaptic development, or even a cellular component – synapse to find highly annotated, semantically linked images in The Cell: an Image Library.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

There are tens of thousands of different biological pathways and each pathway involves complex sets of protein-protein interactions, small molecules, protein complexes, enzymes, regulators and reactions. These pathways are represented in published papers, databases and scientists heads; however now they can also be found on WikiPathways: an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. WikiPathways is a wiki so it is possible to access and contribute biological pathway information easily.

NIF’s federated search engine searches some information in WikiPathways such as pathway name, gene name, gene symbol, or organism. For example, we can search for Wnt signaling pathway in zebrafish (Wnt proteins are part of basic developmental processes, such as cell-fate specification, cell proliferation and asymmetric cell division) using the search syntax “Zebrafish Wnt signaling pathway”.

Categories returned, as mentioned above, are pathway name, gene symbol, gene name, and organism. Clicking on the pathway name will take the users to WikiPathways page for more details on the pathway.

Information on Wikipathways page includes the current diagram, description, references, download options, version history, and component gene and protein lists.

For more thorough instructions on how to use Wikipathways, please visit NIF’s Wikipathways tutorial.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

In previous blog post, we have talked about the importance of C. elegans, or Caenorhabditis elegans, and how its genomic information can be accessed through Wormbase: Genes. In this blog post, we will discuss how we can utilize wormbase to learn more about the anatomy of C. elegans.

Wormbase: Anatomy is an ontology of controlled vocabulary for cellular anatomy. It has short description of an anatomical terms and shows its relationship to other terms in the ontology. Below is a portion of a result returned when gabaergic neuron is searched in the WormBase: Anatomy.

Using NIF, Wormbase: Anatomy can be accessed by searching for specific anatomical terms. For example, if we would like to receive an information on gabaergic neuron like the one above, we can use the search syntax gabaergic neuron. WormBase Anatomy can be found under Nervous System Level -> Cellular Level -> WormBaseAnatomy

Searching in NIF returns anatomical term, its description, expressed genes and affected phenotypes. Clicking on the term will take users to the WormBase: Anatomy page with more detailed information. For more instructions on how to use WormBase Anatomy, please visit WormBase: Anatomy Tutorial.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line atcuration@neuinfo.org.