Tag: Open Data Repositories

Over the past couple of days we’ve looked at the data aggregating capabilities of the Neuroscience Information Framework (NIF). What about literature search? Is there any reason you should move from PubMed or Google Scholar to NIF?

NIF provides the results of a standard PubMed search under the PubMed tab. In addition, NIF provides Open Access Literature, Neuronal Morphology, and Neuroscience Literature tabs. The Open Access Literature tab provides a convenient way to go directly to relevant articles that are freely available over the Internet. The Neuronal Morphology tab provides quick access to papers associated with digitally reconstructed neurons available through NeuroMorpho.org. The Neuroscience Literature tab lists papers returned based on a full text search using your search words. This could arguably the most valuable additional literature search service that NIF provides.

Unfortunately the majority of papers are still published in journals that are not open access. Because of legal restrictions, NIF is only able to provide full text search services on a subset of papers that include those published in open access journals and those published in the Journal of Neuroscience. NIF provides a complete list of journals searched here.

There is a large literature surrounding the amyloid beta protein. Recent evidence suggests that amyloid beta 42 is particularly important in Alzheimer’s disease. What if we only want papers that used amyloid beta 42 in their research? I decided to run a quick test of the full text search capabilities by typing the following “amyloid beta 42” into the NIF home page search box and clicking on the search icon. That didn’t even kick off a search but took me to a blank NEUROLEX page (under neurons and brain regions). The same thing happened when I typed in “amyloid-beta 42” but “abeta42” worked.

Note: All of the variants above worked when I typed them into the search box returned by the initial search from home page (like at top left in Figure 1 above). Surprisingly, searches for “amyloid beta 42” and “amyloid-beta 42” each resulted in zero hits under “Neuroscience Literature.”

A search for “abeta42” returned 161 papers under Neuroscience Literature. I checked all the articles in the first three pages and the last page and they all included abeta42 in the title or the abstract so I’m not sure if we’ve located additional articles that, for example, may have only mentioned the 42 amino acid peptide in its methods section. Also, it doesn’t look like synonyms are being used in the search.

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NIF: When You’re Looking for Neuroscience Resources Including Data

NIF: Neurons, Models, and Grants

Yesterday we took an initial peek at the Neuroscience Information Framework (NIF). Today I’d like to briefly point to the range of Data Federation resources you can find there. When “barrel cortex” is typed into the NIF search box and a search is executed, a couple of subcategories come up under the Nervous System Level category and about five subcategories under Data Type like in Figure 1 below.

In Figure 1 above, the NeuroMorpho: NeuronInfo entry under the Cellular Level subcategory is selected which results in showing a list of some of the 66 neurons from the NeuroMorpho.org repository that are associated with the barrel cortex.

Click on the plus (+) sign to the right of Brain Regions to display entries in that subcategory. The BAMS: BrainRegions entry is associated with an anatomy ontology that provides standard naming conventions for brain structures. The BrainMaps:Atlas entry provides access to relevant high-resolution histology sections. Click on the barrel cortex, barrels link under Brain Region and the BrainMaps.org atlas will appear like in Figure 2 above.

Under the Data Type category, the Images subcategory lists the sites we’ve already looked at. The Models subcategory lists computational model sites relevant to our search. The ModelDB: Models entry lists three models of barrel cortex in the SenseLab ModelDB repository.

You may be puzzled why the Grants subcategory under Data Type shows large number of hits (73 while writing this) but the Grants tab at the top of the section has none. The Grants subcategory provides access to resources on past and currently funded grants. In contrast, the Grants tab provides resources for those wanting to apply for federally funded grants.

Yesterday we looked at resources available under the Microarray subcategory. Our current search brought up 1 resource at the Gene Expression Omnibus (GEO). Finally, under Connectivity you will find information on the known neural connections to and from the brain area or structure you searched on. Tomorrow we’ll take a look at what the NIF Literature tab provides.

Other related blog posts:

NIF: When You’re Looking for Neuroscience Resources Including Data

The Neuroscience Information Framework (NIF) website has become the hub for accessing every type of neuroscience resource from raw data to computer software and research papers. There are two big reasons to make NIF your neuroscience central. First, NIF utilizes the most advanced Web-based informatics technologies available including the Semantic Web so that you may efficiently find what you’re looking for. Second, NIF provides access to resources not typically indexed by search engines so that you’re provided with the most comprehensive Web portal to neuroscience resources available.

In fact, NIF provides so much that it can be overwhelming if you begin by trying to read all of the verbiage about what they provide. As a first step I recommend diving in by using the NIF search box prominently displayed towards the top of the page under “Search for Neuroscience Resources.” For instance, type “EphB2 Alzheimer’s disease” into the search box like in Figure 1 above and press your enter (or return) key or click on the search icon to the right of the box to initiate the NIF search.

A page like the one shown in Figure 2 above should appear. This is a long way from a simple list of matching resources! It can look complicated. However, NIF provides access to a lot of highly focused returned resources in a very logical manner. Let’s take a closer look.

At the top left of the page you should see the “Search the NIF” heading. Under this you should see a search box with the words we entered “EphB2 Alzheimer’s disease” displayed. Under the search box you’re provided options to AND the terms you entered (the default) or to OR the terms. This is followed by a “View/Edit Query” heading, which provides a detailed view of the search construct created and used by NIF based on the search terms you entered. NIF provides you a lot of power by enabling you to modify the “under the hood” query construct if you so desire. Let’s skip this. NIF provides additional power over your search in the panel to the right under the “Search Options” heading. This presents synonyms from NIF’s extensive ontologies. We’ll also skip this for now but it’s good to know you have all of this power available to you.

Note: NIF provides extensive tutorials (including videos) on a lot of its functionality.

Notice the tabs across the top of the next panel down. You should see four tabs including Data Federation, NIF Registry, Literature, and Grants. Each tab heading is followed by the number of hits from your search (in parentheses) within the category. In our case we got 18 hits in Data Federation, which are data sources, and 68 hits in literature.

Note: NIF continues working on your query even after the search results page is displayed. For instance, even though NIF initially returned 68 hits in literature that continued to be added to until it grew to 4,396 hits in literature.

The Data Federation tab displays two categories for the data in our search: Data Type and Nervous System Level. Under the Data Type category, which list experimental data types, you’ll find the Data Type subcategory Microarray. The number associated with Microarray shows you the number of microarray data sets available, which is 18 in this case. Finally, under the Microarray subcategory is listed the data source of which there is only one in this case. All 18 microarray data sets are under Gemma: Microarray which are available through the Gemma online data repository. The other category, Nervous System Level, provides a biology-centric list of available data. In this case NIF has found 18 gene resources associated with the nervous system. The gene resources are all represented by 18 sets of microarray data from the Gemma online data repository. The 18 gene resources are not necessarily different genes. In fact, in our current search they’re all the same EphB2 gene. Each listing does represent a unique gene resource, which in this case is a unique microarray data set from various tissues all from human subjects. You can see this very quickly by scanning the data available to you in the area to the right of the Categories listings. Notice also the ever present availability of tutoring resources (far right).

This has been a brief look at a tiny piece of what NIF provides. NIF is the place to start when looking for neuroscience resources.

Note: Please let me know if you’re interested in hearing more about NIF.