FAQs and Tutorials  

What research resource types can I find in this portal?

In the initial pilot phase we provide four types of resources.

1. Antibodies: primarily commercial antibody reagents, plus a smaller number of lab-sourced ones.
   
2. Organisms: mouse (MGI and IMSR), zebrafish (ZFIN and ZIRC), worm (CGC and Wormbase), fruit fly (BDSC), and rat (RDG) model organisms.
   
3. Tools: software, databases, and services aggregated from a wide range of providers.
4. Cell Lines: Most commercial an non-profit providers are covered as well as lab generated lines.

"Tools" is a broad category that includes software, databases, and services. How do I know which ones to tag?

In order to constrain the problem, we are focusing our pilot project on resources (software, databases, data sets, services) that are listed in the SciCrunch Resource Registry. The SciCrunch Registry focuses on resources largely produced through government funding by academic researchers, but there are some commercial tools listed as well. SciCrunch aggregates data from the INCF Software Center, NITRC, the Gene Ontology tool registry and also lists resources like core facilities. As the pilot develops, we are hoping to add commercial tools as well.

What should I do if my resource isn't available?

First, consult our search tips to make sure that the resource really isn't there rather than it being a search error. Unfortunately, special characters still present a challenge for search. If you have determined that the resource is not there, we provide a minimal set of information that you should provide in any citation for antibodies, tools and model organisms. For model organisms, we refer you to the nomenclature guidelines established by each community. Ideally, however, we would like you to register your resource and obtain a unique identifier.

Should I obtain a unique identifier for commercial software tools?

The current SciCrunch catalog does list commercial tools because you have put them in and our philosophy is: If the tool can introduce substantial variability into your experiment, it is best to add an RRID and version information. So while no publishers requires this, to our knowledge, it is always better to have more RRIDs and commercial tools can give errors the same way as lab made tools can.

Why are there sometimes more than one antibody listed under the same ID?

Because the same antibody is often sold by different vendors. We want to be able to track usage of the antibody regardless of vendor. We use the vendor name and catalog number to identify the particular "version" of the antibody you used, but the unique identifier lets us aggregate all usage regardless of vendor. In many cases we have also aligned data where different aliquot sizes were available from a vendor, or the names of vendors have been updated. This often results in duplicate records, but the proper identifier is assigned to all of them. If you know particular antibody records that should be merged please let us know and we will be happy to merge them.  

Why are some BioSamples linked to RRIDs?

Projects such as the IIDP for pancreatic islets have submitted their cell lines for identification via BioSamples. Additionally, the IIDP wishes to use the RRID resolving services to ask the participants in the IIDP to use the identifiers in their journal articles. The RRID syntax makes this easier as it is enforced consistently across multiple publishers.

Why don’t all BioSamples have RRIDs?

RRIDs are working with BioSamples database in a limited fashion at this time. RRIDs therefore are not available for all BioSamples. If you wish to ask our curators about this please email us at rii-help *at* scicrunch.org

Can I generate new BioSample RRIDs?

If your BioSamples are part of a well organized project such as the IIDP, please contact us rii-help *at* scicrunch.org. As long as the uniqueness of the BioSamples is guaranteed by the project, and the data is aligned well within the BioSample database there should be a means to add your project to the RRID portal.

Tutorials with Full Examples

Finding an Antibody

So let's say you have the antibody "LifeSpan BioSciences Cat LS-C8723-100", and you want to find the identifier. Start by clicking on Antibodies or Any resources.

Usually the catalog number is a unique or close to unique search string so searching for LS-C8723-100 should produce the desired result. In this case there are two records returned, but looking at these carefully one may notice that the identifier is the same. In many cases duplicate records are created where an antibody changes name or vendor, but when we find that these are indeed the same antibody we consolidate the records into one main identifier.

Clicking on the Cite this button will open up a dialog box with the information you need to cite the reagent in your paper. Please copy and paste this information.

My Antibody Does not Exist!

To add a new antibody to the database you will need just two pieces of information: the vendor web site where the antibody information can be found and the catalog number. More information is always better, but our curators will look over and add the information where needed.

http://antibodyregistry.org/add