Registry Overview and Curation Guidelines

If your resource is not listed in our database, you can add it to obtain an RRID for use in the manuscript. SciCrunch systems will track the use of that RRID in the scientific literature. 

SciCrunch registry takes the following types of research inputs:

Software tools

Core facilities

Instruments (capital equipment)

Databases

Tissue banks

Web resources (knowledgebases, atlases, disease focused resources)

SciCrunch registry does not take these types of resources:

Other RRID types - antibodies, organisms please go to https://rrid.site

Datasets - please work with a data repository (search for a repository here)

Chemicals - please consult PubChem for citing these

RNA primers, buffers, consumables, basic lab equipment (pipettes, coverslips etc)

How to cite the SciCrunch Registry

For your methods section:

SciCrunch Registry, RRID:SCR_005400

For your references section:

Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature. PLoS One. 2016 Jan 5;11(1):e0146300. doi: 10.1371/journal.pone.0146300. PMID: 26730820; PMCID: PMC5156472.

When citing any resource within the SciCrunch Registry, please use the provided “proper citation” field in the methods section.

Curation Guide for SciCrunch Registry

SciCrunch Registry Overview

The SciCrunch Registry, is proud to be the source for RRIDs for web resources that have been contributed by the community. The SciCrunch Registry contains a listing of a variety of resources including databases (which store scientific data), software tools (both commercial like MATLAB and lab generated like Jupyter Notebooks), core facilities (which create tools or conduct specific analyses for the study), instruments (capital equipment), scientific atlases, and tissue banks. Resources are continually added and updated by SciCrunch's staff, affiliates, and authors who need RRIDs.

SciCrunch Registry Vocabularies Used

The SciCrunch Registry uses SciCrunch vocabularies to provide high-level descriptions of the nature of the resource and its contents. Searching for global key words such as "genes" or "tissue bank" will bring up the various resources that have those descriptors, whereas "GRM1" or "C57BL/6J-rcw3J/J" will not bring up results, as the specific gene name or strain names are not tagged for each resource. The SciCrunch Registry is a place where there is a list of Alzheimer's disease tissue banks, but it will not tell the user which types of tissues are found in each tissue bank. Currently the URL fields are not searchable, but if you are adding a new resource a URL may match an existing resource.

SciCrunch Registry Submission of new Resources

All records are curated by SciCrunch curators to comply with our policies, but community involvement is highly encouraged. Anyone may add a new resource, and the community can let curators know that a resource is out of date by leaving a message. Resources can be edited by curators and resource owners. 

Anyone, whether it is the resource owner or not, may register any resource. If you are the resource owner you may claim ownership (separate action described below), we encourage owners to the how to cite my resource using the RRID on your tool’s website.

Click on the “Resource” part of the “contribute” webpage.  The registration form asks for three required pieces of information: name of the resource, URL, and description. You may fill in additional fields, but this is not required. 

The curator will get back to the submitter either approving the resource, rejecting the entry, or asking additional questions within 1 working day.

Once approved, the resource will be assigned an RRID. It will also be included in the SciCrunch Registry (please allow 48 hours after you receive the letter from curation before contacting the registry as the nightly update “job” may not include your resource until the following day). 

As a general rule, users should register a root/individual resource and not a subset of that root/individual resource. It shall be considered an individual resource if it is maintained by a single entity, and has the properties of one or more individual web pages that are related by a theme and HTML links. Most often the individual pages share portions of the URL, however, unrelated URLs may be incorporated into a single web resource as alternate URLs. In the event that a subgroup of pages represents a sufficient shift in theme, it should be classified as an independent resource. For example, a laboratory created a sequence alignment software tool (resource 1) and this tool works with a database of sequences (resource 2). If the tool and the database can be used independently, have independent funding and need to be tracked separately then they should be two resources. Registering them as one resource may be appropriate, but the curator will likely ask questions of the submitter. 

Resource Creators (owners): People who created or maintain a resource can claim ownership (can be thought of as authorship) to help us maintain the webpage and gain additional rights to edit the resource. 

• In order to claim ownership, you must first log into your account.

• Search for your resource and click the name of your resource to get to a page like this

• Click the “Claim Ownership” button and follow the prompts. It will ask for some proof that you are the owner like authorship of a paper, your picture or email consistent with a core facility webpage etc.

What can be included in the SciCrunch Registry?

The SciCrunch Registry is not exclusive to any one type of resource. However, we do not include all resources. The rule of thumb for SciCrunch staff is that if the resource is described in a methods section of a scientific paper generally as an input to the study, then it can be included.

Some classes of resources, such as consumables (chemicals), electronic journals, datasets, and any resources that already have a specific RRID type, are generally not included in the SciCrunch Registry. 

All resources may have a list of fields associated with the resource. Specific resource types listed below must follow naming rules and conventions. 

Curated field names are listed below along with guidelines for inclusion of information, but other field names such as social media handles may be used. If a field does not exist that you would like to use, please contact us. 

Fields available for any resource:

1. Name: Try to name resources just as they are presented on the website with regards to capitalization and spacing e.g., "PubMed" would not be "Pubmed", or "Pub Med".

Additional rules include: If a resource begins with "The" drop it when naming the resource unless the abbreviation incorporates the T. 

Do not make up names, synonyms or abbreviations unless you feel these alternate names will be searched for to find the resource. 

Do not use colons, quotation marks, @, brackets or ampersands in a resource name as these create problems, including resources being unable to be tagged "curated". Synonyms can be used to circumvent this problem. (@ and brackets ([]) cannot be used at all in any of the forms fields)

Avoid special characters like "/", ":"as no one will query for them.

Do not use version numbers as these will change over time

Avoid extra description in the title. Remember, these will be used for search and for alphabetizing. The name of the resource should be the common name:

Yes: “Flybrain” - No: “FlyBrain - An Online Atlas and Database of the Drosophila Nervous System.”

2. Description: The description should be one to two sentences. It can often be paraphrased or copied from the "about us" section of the resource or from its home page.

First sentence: Noun with basic core function. EX: Source code that performs multiple alignment of peptidic sequences.

Note for first sentence: The first word(s) should generally be a statement of the classification used by the SciCrunch curator for resource type. If the resource is classified as a data set, the first line should read "Data set that...". If it is a software application, it should read "Software application..." These may be changed slightly for grammatical or readability issues, but it is good practice that the human readable definition and the machine readable definition should be the same.

Second sentence: Concise expansion on core function. EX: It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

While it is tempting to copy the description of the resource verbatim from the web site, please do not do this indiscriminately. Rather, turn them into informative, pithy, machine-readable resource descriptions. These descriptions will be displayed as snippets by many tools that access the resource registry. Thus, the first line of the description should be as informative as possible.

Example: Let's say we wanted to add a resource that is called: Cow brain gene expression atlas

Good leading sentence: Atlas detailing the three dimensional expression of 20,000 genes across major regions of the cow brain.

Bad leading sentence: The Cow Brain Gene Expression Atlas was developed by the University of X and aims to provide an increased understanding of ..."

The following are guidelines and best practices for reviewing and writing resource descriptions:

• Do not repeat the name of the resource in the first sentence

• Avoid using the personal pronoun when describing the resource, as SciCrunch's descriptions should not be from the resource provider's point of view, e.g., do not say "We offer...".

• Please remove any brackets or @ that are in the description, e.g., for references, email addresses, as these are interpreted by the Wiki and lead to errors in formatting (@ can be replaced with (at) or at)

• Make sure to eliminate any breaks or spaces that might be introduced by copying HTML.

• Avoid using terms that have a time component, e.g., "new", "recently", because these can become out of date and misleading pretty quickly.

• Remove any qualifiers used in the resource description that are subjective and not-informative, e.g., cutting-edge, most comprehensive available, global leader. Pay particular attention to this policy if you are curating a commercial site. Their descriptions have been written by public relations experts, not scientists.

3. Resource URL Add the URL of the resource including the http:// portion of it; i.e., adding a URL such as www.neuinfo.org will not link. You must provide the full URL, http://www.neuinfo.org/.

The URL should only include the necessary portion required to function, e.g., use http://neuromorpho.org/neuroMorpho/ rather than http://neuromorpho.org/neuroMorpho/index.jsp. Use https://www.niddkrepository.org/ rather than https://www.niddkrepository.org/home/. That said, please verify that the trivial portion of the URL is indeed not needed. Surprisingly, some URLs will not work without these.

Some websites have multiple URLs pointing to the same resource. Separate multiple alternate URLs with a comma ",". These alternate or old URLs may often be found in the abstract section of the resource’s associated paper.

Refer to SciCrunch’s Link checking policy below when a new URL cannot be found for the resource.

4. Keywords: Keywords should be used to supply related terms that characterize the resource that may or may not be in the ontology. Keywords should be "meaty", that is, they should convey specific information content and be likely search terms, e.g., proteomics, is a good keyword, as people are likely to search for that and we do not list it as a resource type. Please note that while they should be "meaty" they should not be too specific. They should be probable search terms but should not encompass every possible function and detail.

Avoid generic keywords like "experiment", "species", "science", "discipline". Use the keywords for ancillary functions of a resource, e.g., ModelDB imports and exports models for simulation. It isn't a "simulation resource", as it is not used as a platform for simulation. It is, however, related to simulation and that would be an acceptable keyword.

Keywords should use the singular form for the word and, if applicable, cover things such as:

• Technique: microscopy type, assessment test, behavioral data, electrophysiology etc.

• Structures covered: sub-cellular components, cells, brain regions, body structures, whole animals etc.

• Topic covered: psychology, neurology, neuroscience, physiology, behavior, etc.

• Functional level: embryonic, young, adult, aging

Information, as far as possible, must be machine readable and human readable. Therefore, do not just copy terms, but curate them. 

Good Example: Longitudinal fasciculus, medulla oblongata 

Bad Example: LF, MO. Avoid abbreviations unless they are widely conventional and reasonably unambiguous such as fMRI.

5. Defining Citation: PubMed IDs or DOIs of papers about the resource should be added to this field. Do not add papers that reference the resource or only mention the resource. We have an automated service that collects these mentions. Multiple IDs may be separated by a comma. If the resource does not have a PMID number, use the Publication Link field to enter the url of the digital journal article. Separate each paper entry by a comma. 

Example: PMID:25018728, PMID:23195120 

6. Abbreviation: The abbreviated name will be used to identify your resource in publications and it is unique. Please make sure that a page with the name does not currently exist.

7. Synonyms: Include variations of the name that are used in the website or associated paper. Save abbreviations for the Abbreviation field.

8. Funding Information: Include information related to the resource's funding information (supporting agency and funding support). Separate multiple grants by a comma. Format-Supporting Agency+ space+funding support number.

Example NIH Office of the Director 000000000, Contract HHSN27120080035C

9. Comment: This field is for the user to submit any comments about the submitted resource. This will not be displayed on the public resource webpage.

10. Editorial Note: This field is for the curator to make any additional comments about this resource. This field is also not displayed on the resource webpage.

11. Additional Resource Types: Additional resource types have been created to provide a standardized method of classifying resources. Resources should be labeled with the main thing(s) that the resource offers using terms within the Resource Type Hierarchy

Please label the primary product, that is, what would a user expect to take away from this site? Avoid assigning resource types for very minor functions. 

These resource descriptors are meant to narrow search results by the type of thing that a scientist is looking for. 

The resource should be tagged with all applicable resource types, but for minor functions use the Keywords field. 

12. Availability: State the availability of the resource/licensing information. E.g., if the resource is a biobank, can anyone request biomaterials? Is it public, open source, freely available but must cite, freely available to academic institutions, etc.? If available, this information can be obtained either from the website or the related article.

If the resource is no longer available, please add the following to this field as well as to the top of the description: THIS RESOURCE IS NO LONGER IN SERVICE, documented on ‘full month’ ‘day’, full year. (e.g., THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 05, 2013.). When adding this to the Availability field, remove all punctuation so that it is recognized as one statement by the computer. If the user can add to the resource, add "The community can contribute to this resource" in the field.

13. Terms of Use URLs: The URL(s) where the resource posts under which conditions you may use the resource. This can include other titles, e.g., copyright page, citation policy, policy, terms and conditions, etc., (comma separated for multiple entries). This field should not include the url of the actual license. (The actual license has its own entry with associated url (s)).

14. Alternative URL: Other/Alternate URLs that retrieve the source (comma separated for multiple entries).

15. Old URLs: URLs that used to retrieve the source but no longer work (comma separated for multiple entries).

16. Alternative IDs: A list of comma separated identifiers, DOIs, FairSharing IDs, GRIDs are all allowed.

17. Related Application: This field was created primarily for the biospecimen resources to state if the bioresources were to be used for research, transplantation, therapy, education etc. Multiple entries are to be separated by a comma.

18. Related Disease: If the data resource concerns a disease, set of diseases, or condition, make sure that they are stated (e.g., Parkinson’s disease, neurodegenerative disorder, Batten’s disease, Aging, Normal control, etc.). Additional entries are to be separated by a comma.

19. Located in: The physical location that the resource is located in.

20. Processing: This field is mainly used for biobanks and what sort of processing the biospecimens have been put through, e.g., Frozen, paraffin, slide, cryopreserved, stained, fresh, etc. Separate multiple entries by a comma.

21. Species: Add organisms represented in the resource, E.g., if the resource is a database of mouse gene expression, add “mouse” to this field. Not all resources will have an associated organism; e.g., like many software resources. Some resources are not forthcoming with this information. For instance, if the database is a clinical trial database, make sure that it is labeled “human”. Many resources mention the organism(s) in the description, but as some do not, it becomes very important to capture this information. Multiple organisms may be added; just separate them with commas.

22. Supercategory: This is the primary resource type. Entries will either be a resource, commercial, an institution or a university.

23. Publication Link: Occasionally there is a PDF or other publication that is about the resource. You may also link directly to the paper, even if it is in PubMed. This field will only accept one URL. Please include the full URL that includes the http:// (or the like) part for the link to work.

24. Social URL: Add the social url for this resource, for example FaceBook, Google+ and WordPress.

25. License: This field is dedicated to the terms under which the content is made available. Place a short description about the licenses used.

26. Twitter Handle: Only the twitter handle should be used for this field. For example, @Twitter::neuinfo. The twitter handle “neuinfo” should be used.

27. Related to: Resources within SciCrunch may be related to one another. The following public gray “box” conveys that a resource is related to two other resources. The green “box” is on the edit page where relationships and other resources may be selected.

Specific "Related To" categories are: Uses <-> Is Used By, Recommends <-> Is Recommended By, Lists <-> Is Listed By, Is Affiliated With, Is Related To, Has Parent Organization <-> Is Parent Organization Of, Requires <-> Is Required By and Duplicate Of. 

Is Affiliated With - a resource is associated with, or involved in, another resource. This category is typically used to connect consortium members to their respective consortiums.

Duplicate Of - is a special category that removes the duplicate resource. The Duplicate box is only marked for the duplicate resource with younger/most recent Original ID.

Parent Organization: The institution that houses/maintains the resource, for example the Allen Brain Atlas is housed at the Allen Brain Institute. A physical address can be associated with the parent resource. The parent organization should be the university as opposed to a department.

Special considerations for specific types of resources:

Equipment/Instrument data input to the SciCrunch Registry. 

Equipment/Instrument Names. Enter the equipment name following this pattern:

    [Manufacturer] [Model name and/or number] [Equipment Classification]

Example 1: Bruker Avance III NMR spectrometer console

Example 2: Tecmag TD3-RF1 broadband linear radio frequency power amplifier 

Instrument System Names. Enter manufacturer configured systems the same as for Equipment Name.

[Equipment System Classification] [Specifications of primary equipment classification with indication of other equipment or the system's function]

Example: Bruker Avance III 500 NMR spectrometry system

Example: NMR spectrometry system: 800 MHz/52 mm superconducting electromagnet with Cryo Probe

[Equipment System Classification] = NMR spectrometry system [Specifications of primary equipment] = 800 MHz/52 mm [Classification of primary equipment Other equipment] = Cryo Probe

What is entered in the middle section of the name will vary depending on the type of equipment and the system's configuration. Use your best judgment. Please type the equipment model as it appears on the machine and is commonly referred to. The model number should be distinctive and easy to search for.

Additional Resource Type: Use "Instrument resource" as Additional Resource Type for equipment.

Keywords as standard words: Add "ABRF"

Alternate IDs: Add equipment Model Number information under.

Comments: Add equipment Manufacturer and Brand information under Comments if manufacturer manual or brochure in pdf format is not available.

Alternate URL: Add manufacturer manual or brochure in pdf format.

Availability: When you have a piece of equipment that is no longer in service, as opposed to deleting the equipment place a note in the description that states the equipment is no longer active as of a certain date. Example: THIS EQUIPMENT IS NO LONGER AVAILABLE AS OF 8/17/2016.

Organizations:

Ideally every organization such as a university or medical school should be pulled directly from ROR.org. 

Names: Universities located in the United States should be written as follows:

[University Name]; [State]; [USA]

Example: Cornell University; New York; USA

Universities located outside the United States should be written as follows:

[Name]; [City/State/Province] (1st choice=state, 2nd=province, 3rd=city); [Country]

Example: University of Oxford; Oxford; United Kingdom

Example: University of Alberta; Alberta; Canada

Additional Resource Types Use: University, Institution, Commercial Organization or Nonprofit Organization (some organizations that are needed may not have a ROR)

Alternate URLs: Use the full ROR URI format like this https://ror.org/05hr6q169 

Alternate IDs: List all known identifiers example: nlx_156945, grid.7048.b, Crossref funder ID: 100007605, ISNI:0000 0001 1956 2722, Wikidata:Q924265

Supercategory: always use Organization

Please note, not all RORs for universities are unique so please report any problems to ROR when you find two or more ROR identifiers for any university. Map the registry entry to the final ROR id. 

For commercial organizations, the SciCrunch Registry assigns a single RRID to the organization as a whole; individual services within the company do not receive separate RRIDs. However, information about these services can be included in the organization’s description. 

University Core Facilities:

To obtain an RRID for a core facility, the facility name must match the name on its dedicated core webpage, and the name and email address of a contact person must be listed. Once assigned, the RRID should also be added to the core’s webpage to make it easier for users to include it in the manuscripts. 

If you are a core owner/contact person, please consider adding the RRID to your email signature for the main email address with which your team communicates with your users. These steps seem to be highly effective ways to get users to cite you!

SciCrunch Registry partners with ABRF’s Core Marketplace. Core Marketplace enables people to find core services, while the RRID entry is centered around usage tracking. You can obtain RRID for the core by sending the request to the SciCrunch Registry or the CoreMarketplace. We exchange information and the RRID will appear on both pages.

As the RRID is intended to be a way to cite your service, please encourage your users to cite you using the RRID by:

• Adding the RRID to your website with a request for users to cite it.

• Include RRID citation instructions in your staff’s standard email communications with users.

• Provide the RRID citation format in any methods or acknowledgments sections of manuscripts you assist with.

RRIDs are effective for tracking resource usage only when they are used consistently.

Commercial Organizations:

For commercial organizations, the SciCrunch Registry assigns a single RRID to the organization as a whole; individual services within the company do not receive separate RRIDs. However, information about these services can be included in the organization’s description. 

The CoreMarketplace can assign the ABRF_IDs to the commercial organization individual services.

RRID listings are not meant to serve as advertisements. Please describe what your organization does (e.g., "We analyze blood samples for heavy metals") rather than use promotional language (e.g., "We are a world-leading analytics platform"). Marketing content will be removed during the curation process. Please allow 3–4 business days for curation. Once complete, you’ll receive the proper citation format, which will be displayed on your new RRID webpage.