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.

C. elegans, or Caenorhabditis elegans, is a one of the most popular model organism used in biomedical research. Transparency, ability to be frozen, and easy and cheap breeding all make C. elegans an ideal model for research.

In this blog post, we will look into WormBase’s gene database of C. elegans. Wormbase provides up-to-date informations regarding genomics and biology of C. elegans. Their vast amount of data, including genes, proteins, expressions, phenotypes, sequence, ontology etc, are both applicable to biologists and computer scientists.

Using NIF, Wormbase: Genes can be accessed by searching for specific gene name. For example, we can search for the gene pcn-1 (Search syntax = gene:pcn-1). WormBase Genes can be found under Nervous System Level -> Genes

Above image is the result of the search. It gives you gene, description, expression, Gene Ontology info, KOG Functional info and phenotype. Clicking the gene will take you to the WormBase gene for more details. For more information on how to WormBase Genes, please visit WormBase Genes 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.

“A picture is worth more than a thousand words”. This idea applies to neuroscience and emphasizes the importance of visualization in science. With one image, it is possible to easily extract information and data that can take many words and tables to describe. XNAT, Extensible Neuroimaging Archive Toolkit is an open source imaging informatics platform designed to facilitate management and exploration of medical imaging and related data.

XNAT offers a set of human brain MRI images and its associated data, such as gender, age, clinical dementia rating and socioeconomical status. These associated data give users flexibility on how images can be searched. For example, you can search for brain images of female who is 84 years old (Search syntax: Female Age 84/ AND terms) or you can search for brain images for certain disease, such as alzheimers(Search syntax: Alzheimer’s). XNAT data can be found at Data Type -> Dataset -> XNAT: MRIStudies

Above image is the search result for “age 84 female”. Clicking on the subject id will take you to XNAT’s website with more information on your subject. These images can be viewed online through XNAT’s browser or can be downloaded freely to your hard drive. For more information on how to use XNAT, please visit XNAT 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.

We have talked about ZIRC, Zebrafish International Resource Center, in NIF blog before (ZIRC Data Spotlight). ZIFN, Zebrafish Model Organism Database, is a sister organization of ZIRC.  ZIRC provides services and resources you need to run zebrafish experiments, whereas ZIFN offers an online database of genetic and developmental information. Contents offered by ZIFN includes genetic markers, BLAST, genome browser, gene expression, antibodies, ontological information, publications, and much more.

In NIF, ZIFN database can be accessed through specific gene like we did in ZIRC or it also can be accessed through brain region or neurons. For example, we will search for information about zebrafish’s midbrain.

With above search syntax, NIF returns various information found in its Data Federation. ZIFN database can be found under Nervous System Level -> Genes -> ZIFN: Gene Expression, or under Data Type -> Genes -> ZIFN: Genes. Gene Expression tab will show gene, genotype, structure, start and end stage, and assay. Genes tab will show Genotype, stages, affected structure or process, publication, phenotype, and environment.


For full tutorial on ZIFN please visit here.

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 Allen Mouse Brain Atlas is an interactive, genome-wide image database of gene expression. The Neuroscience Information Framework returns quantitative expression values on a gene by brain region basis.

We can begin searching for a gene by typing – “htrb” into NIF.

Using the NIFSTD ontology, our search for the serotonin receptor B is expanded to all known synonyms for this receptor.

Found under Nervous System Level >Genes and Data Type > Images, we have returned 51 records from the Allen Brain Atlas.

The results are organized by gene symbol and include organism and structure data, when available. Expression data are give as two values, both are normalized to 100%. To find out more information about the methods used to obtain expression values please refer to the Allen Brain site documentation.

Clicking on any Gene Symbol will open the record detail on the Allen Brain Atlas site. Here you have many options to switch between ISH, Expression Mask or Composite views of associated image. For more information please visit our Allen Brain Atlas tutorial.

The Aging Genes Database, provided out of the University of Washington, contains information on genes and interventions that have been studied in respect to their effects on life-span or age-related neurological diseases.

A quick overview of the data reveals that approx. 100 records have a life-span extension phenotype and approx. 20 describe a “shortened life-span” effect. Moreover, the top species represented in the Aging Genes DB are the Fly (D. melanogaster), Worm (C. elegans) and Mouse (M. musculus) (shown below). For more information of how to access NIF Data Federation summaries (used to make the graphs below) see our tutorials on NIF REST Services.

We currently index two views on the Aging Genes Database: Genes and Interventions. The genes view targets aging phenotypes of particular genes. For example, to search for the gene encoding Apolipoprotein E we can search for “gene:ApoE” at neuinfo.org;

The Aging Genes Database can be found under Nervous System Level > Genes. Here we discover that ApoE is correlated with higher cholesterol levels, cardiovascular disease and is a risk factor for cognitive impairment under age 85.

Clicking on the Gene Name will open the Aging Genes Database, where you will have to select the gene once more to get additional information.

On this page, we are given summary data for ApoE, with links to Pubmed and NCBI gene.

For more information on the Aging Gene Database, as well as a tutorial to access the Aging Interventions data – see our tutorial here.

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.

For a number of reasons, the use of zebrafish in neuroscience research is steadily on the rise. At the Neuroscience Information Framework, we have recognized this trend and have active lines of communication with several zebrafish information providers. The Zebrafish International Resource Center (ZIRC) is the premier source for wild-type, mutant, and transgenic zebrafish strains as well as laboratory methods and husbandry techniques for zebrafish investigations.

NIF enables you to find a mutant zebrafish strain easily using gene specific search techniques. For example, clasp1 is a cytoplasmic linker protein involved in the regulation of microtubule dynamics, particularly in the brain and heart. Animal models with functional changes in clasp1 may be of interest to neuroscientists investigating synaptic changes that occur during LTP or other neurobiological aspects of learning and memory.

To focus our search to genes, we use the following search syntax “gene: clasp1” (shown above). This returns a number of results from across the NIF data federation, including Datasets and Antibodies. Results from ZIRC may be found under Animals > ZIRC: Zebrafish from which you are one click away from purchasing zebrafish and getting your aquatic laboratory up and running. For more information about ZIRC and NIF, please see our detailed 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.

We have all been there before. Whether learning or re-learning the basic biology of DNA plasmids, figuring out the best plasmid for your line of research can be a difficult task.  This week’s featured NIF database, AddGene, is greatly improving this process. AddGene maintains a high-quality plasmid repository which allows researchers to submit and deposit plasmids. These plasmids are then cataloged and linked to published articles so that scientists can easily find data and other information related to the plasmid of interest.

The “Brainbow” Nature article, “Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system” by Livet et. al. (2007) provides an illuminating example.  By exploiting the Cre-Lox recombination system, these researchers were able to induce stochastic expression of several fluorescent proteins across a population of neurons. As a result of the Brainbow transgenes, individual neurons and their projections become labeled with a distinct color.  This strategy, therefore, provides a novel way to visualize neuronal network architecture with precise detail and significantly improves computer-aided tracing of cellular interactions (see figure below).

Ready to add some color to your research? No problem with the help of AddGene! A quick search for “Brainbow” at Addgene provides all the information necessary to evaluate and purchase each of the Brainbow transgenes discussed in our article. At NIF, the AddGene database is a registered resource of the NIF data federation and search results can be found under Data Type > Plasmids. For additional information about NIF and AddGene, we have an example available at NIF Tutorials.

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.