Funder/Policy Analysis for Nihms Deposit

[tsande16]

Justification/Why

• Adding the funder to the submission to the NIHMs will speed up their workflow process.
• Figuring out the best way to map a funder to agency code required by NIHMS will make PASS more extensible in the future.

Goals:

• Need to analyze the funders and discuss with nihms about which center that roll up into the NIH.
• Depending on the outcome of the discussion with nihms, may need to change the PASS data model. Will need to discuss with the team how funder/policy should be realized given the funder realization by nihms.

Questions:

• Should the policy dictate which nihms recognized funder code?
• Should the pass_funders have a column such as federal_agency which would align with the values provided by the nihms funder codes.
• Should the federal_agency be an attribute to the pass_policy? The policy is dictated by the federal_agency, might make the most sense to have it be an attribute of the agency. There already seems to be an unused column institution which we could use. Although this language is used by NIH to refer to the individual organizations that are part of the NIH.
• Should we have a new entity of a "federal agency"? In terms of NIH organization/nomenclature many funders are called a center or institute that are part of the NIH.
• Should it come from the pass_funders and if that is the case given the many sub agencies of the NIH, will need verify with nihms that each one should get the nih code.

Notes: The Nihms DTD validates the following funder codes: ( nih | ahrq | aspr | cdc | epa | fda | hhmi | nasa | nist | va ). As @dkriethof noted, some of these are no longer supported. Really at the moment for ticket #828 we are only concerned if the list of funders below roll up into the nih abbreviated code in the DTD. The realization of this business logic will determine how we should handle it in deposit-services

Funders in PASS:

NATIONAL LIBRARY OF MEDICINE
NATIONAL INSTITUTE ON AGING
NATIONAL INSTITUTE OF MENTAL HEALTH
NATIONAL CENTER FOR ADVANCING
NIH CLINICAL CENTER
NATIONAL INSTITUTE ON MINORITY HEALTH
FOGARTY INTERNATIONAL CENTER
NATIONAL INSTITUTE OF DEAFNESS AND OTHER
NATIONAL CANCER INSTITUTE
NATIONAL INST OF GENERAL MEDICAL SCIENCE
NATIONAL INST OF DIABETES AND DIGESTION
OFFICE OF THE DIRECTOR NIH
NATIONAL HUMAN GENOME RESEARCH INSTITUTE
NATIONAL INSTITUTE OF BIOMEDICAL IMAGING
NATIONAL INSTITUTE ON DRUG ABUSE
NATIONAL INST OF NEUROLOGICAL DISORDERS
NATIONAL INSTITUTE OF ARTHRITIS AND
NATIONAL EYE INSTITUTE
NATIONAL INSTITUTE OF ALLERGY AND
NATIONAL INSTITUTE OF DENTAL AND CRANOFA
NATIONAL INST OF CHILD HEALTH AND HUMAN
NATIONAL CENTER FOR COMPLEMENTARY AND
NATIONAL INSTITUTE OF NURSING RESEARCH
NATIONAL HEART LUNG AND BLOOD INSTITUTE
NATIONAL INSTITUTE ON ALCOHOL ABUSE AND
NATIONAL INSTITUTE OF ENVIRONMENTAL
NATIONAL INSTITUTES OF HEALTH

Centers/Institutes of NIH: https://www.nih.gov/institutes-nih/list-institutes-centers

[dkriethof]

Related to "Notes: Nihms recognizes the following funder codes: ( nih | ahrq | aspr | cdc | epa | fda | hhmi | nasa | nist | va )"

Per an email from Pierce (from Oct), we should be supporting NIH, AHRQ, ASPR, CDC, EPA, FDA, HHMI, VA but seems like that list is missing:

• [ ] ACL
• [ ] Bill & Melinda Gates Foundation
• [ ] HRA

We were also supposed to remove NASA and NIST (per your list, seems like we already removed DHS).

from his email: PASS should NOT support: DHS, NIST, or NASA Because of DHS policy, only DHS funded papers can only be accepted by PubMed from DHS NIST is similar to DHS NASA no longer deposits manuscripts in PMC

Not sure this is relevant to this discussion/ticket, but I noticed the list didn't seem up to date.

[tsande16]

@dkriethof The list provide is the DTD that nihms uses for validation. It's the most up-to-date DTD that we received from them. It's possible they still keep those values in their DTD for backward compatibility reasons.

[tsande16]

For more information about the funders (sourced from pass_funders) and their mapped policy. Added a new column which is the abbreviation used by NIHMS.

funder_id, funder_name, policy_id, policy_title, assumed_agency_abbr
43154   "AGENCY FOR HEALTHCARE RESEARCH"    41582   "Agency for Healthcare Research and Quality Public Access Policy"   "ahrq"
44182   "CENTERS FOR DISEASE CONTROL"   41588   "Centers for Disease Control and Prevention Public Access Policy"   "cdc"
43765   "NATIONAL INSTITUTE FOR OCCUPATIONAL"   41588   "Centers for Disease Control and Prevention Public Access Policy"   "cdc"
43680   "US DEPARTMENT OF VETERANS AFFAIRS" 41586   "Department of Veteran Affairs Public Access Policy"    "va"
43607   "ENVIRONMENTAL PROTECTION AGENCY"   244022  "Environmental Protection Agency Open Data Policy"  "epa"
43797   "HOWARD HUGHES MEDICAL INSTITUTE"   41580   "Howard Hughes Medical Institute Public Access Policy"  "hhmi"
44612   "FOGARTY INTERNATIONAL CENTER"  41587   "National Institutes of Health Public Access Policy"    "nih"
45453   "NATIONAL INSTITUTES OF HEALTH" 41587   "National Institutes of Health Public Access Policy"    "nih"
41932   "NATIONAL INSTITUTE ON AGING"   41587   "National Institutes of Health Public Access Policy"    "nih"
42891   "NATIONAL INSTITUTE OF MENTAL HEALTH"   41587   "National Institutes of Health Public Access Policy"    "nih"
42965   "NATIONAL CENTER FOR ADVANCING" 41587   "National Institutes of Health Public Access Policy"    "nih"
42626   "NIH CLINICAL CENTER"   41587   "National Institutes of Health Public Access Policy"    "nih"
44569   "NATIONAL INSTITUTE ON MINORITY HEALTH" 41587   "National Institutes of Health Public Access Policy"    "nih"
48010   "NATIONAL INSTITUTE OF ENVIRONMENTAL"   41587   "National Institutes of Health Public Access Policy"    "nih"
41679   "NATIONAL LIBRARY OF MEDICINE"  41587   "National Institutes of Health Public Access Policy"    "nih"
44733   "NATIONAL INSTITUTE OF DEAFNESS AND OTHER"  41587   "National Institutes of Health Public Access Policy"    "nih"
44425   "NATIONAL CANCER INSTITUTE" 41587   "National Institutes of Health Public Access Policy"    "nih"
46772   "NATIONAL INST OF GENERAL MEDICAL SCIENCE"  41587   "National Institutes of Health Public Access Policy"    "nih"
46842   "NATIONAL INST OF DIABETES AND DIGESTION"   41587   "National Institutes of Health Public Access Policy"    "nih"
45199   "OFFICE OF THE DIRECTOR NIH"    41587   "National Institutes of Health Public Access Policy"    "nih"
45571   "NATIONAL HUMAN GENOME RESEARCH INSTITUTE"  41587   "National Institutes of Health Public Access Policy"    "nih"
46149   "NATIONAL INSTITUTE OF BIOMEDICAL IMAGING"  41587   "National Institutes of Health Public Access Policy"    "nih"
46383   "NATIONAL INSTITUTE ON DRUG ABUSE"  41587   "National Institutes of Health Public Access Policy"    "nih"
46386   "NATIONAL INST OF NEUROLOGICAL DISORDERS"   41587   "National Institutes of Health Public Access Policy"    "nih"
46388   "NATIONAL INSTITUTE OF ARTHRITIS AND"   41587   "National Institutes of Health Public Access Policy"    "nih"
47169   "NATIONAL EYE INSTITUTE"    41587   "National Institutes of Health Public Access Policy"    "nih"
47227   "NATIONAL INSTITUTE OF ALLERGY AND" 41587   "National Institutes of Health Public Access Policy"    "nih"
47229   "NATIONAL INSTITUTE OF DENTAL AND CRANOFA"  41587   "National Institutes of Health Public Access Policy"    "nih"
47367   "NATIONAL INST OF CHILD HEALTH AND HUMAN"   41587   "National Institutes of Health Public Access Policy"    "nih"
47555   "NATIONAL CENTER FOR COMPLEMENTARY AND" 41587   "National Institutes of Health Public Access Policy"    "nih"
47689   "NATIONAL INSTITUTE OF NURSING RESEARCH"    41587   "National Institutes of Health Public Access Policy"    "nih"
47866   "NATIONAL HEART LUNG AND BLOOD INSTITUTE"   41587   "National Institutes of Health Public Access Policy"    "nih"
47910   "NATIONAL INSTITUTE ON ALCOHOL ABUSE AND"   41587   "National Institutes of Health Public Access Policy"    "nih"
42620   "OFFICE ASSISTANT SECRETARY PREPAREDNESS"   41578   "Office of the Assistant Secretary for Preparedness and Response Public Access Policy"  "aspr"
42276   "FOOD AND DRUG ADMINISTRATION"  41583   "US Food and Drug Administration Public Access Policy"  "fda"

[tsande16]

I verified with Pierce and this listing, that all the funders are part of the NIH: https://www.nih.gov/institutes-nih/list-institutes-centers

All of these institutes/centers below are part of the NIH, although some of them have their name truncated e.g. NATIONAL CENTER FOR ADVANCING

NATIONAL LIBRARY OF MEDICINE
NATIONAL INSTITUTE ON AGING
NATIONAL INSTITUTE OF MENTAL HEALTH
NATIONAL CENTER FOR ADVANCING
NIH CLINICAL CENTER
NATIONAL INSTITUTE ON MINORITY HEALTH
FOGARTY INTERNATIONAL CENTER
NATIONAL INSTITUTE OF DEAFNESS AND OTHER
NATIONAL CANCER INSTITUTE
NATIONAL INST OF GENERAL MEDICAL SCIENCE
NATIONAL INST OF DIABETES AND DIGESTION
OFFICE OF THE DIRECTOR NIH
NATIONAL HUMAN GENOME RESEARCH INSTITUTE
NATIONAL INSTITUTE OF BIOMEDICAL IMAGING
NATIONAL INSTITUTE ON DRUG ABUSE
NATIONAL INST OF NEUROLOGICAL DISORDERS
NATIONAL INSTITUTE OF ARTHRITIS AND
NATIONAL EYE INSTITUTE
NATIONAL INSTITUTE OF ALLERGY AND
NATIONAL INSTITUTE OF DENTAL AND CRANOFA
NATIONAL INST OF CHILD HEALTH AND HUMAN
NATIONAL CENTER FOR COMPLEMENTARY AND
NATIONAL INSTITUTE OF NURSING RESEARCH
NATIONAL HEART LUNG AND BLOOD INSTITUTE
NATIONAL INSTITUTE ON ALCOHOL ABUSE AND
NATIONAL INSTITUTE OF ENVIRONMENTAL
NATIONAL INSTITUTES OF HEALTH

[tsande16]

From our discussion today:

Next steps:

• Perform research about a standard set of funder identifiers
  • Investigate using the Open Funder Registry: https://www.crossref.org/services/funder-registry/
  • Criteria for selecting a database of funders: Active supported community? Other orgs use this for their list of funders?
• Once an indentifer source is established there are couple of ways to implement:
  • Use a URI as an identifier
  • Will still need to map the agency URI to the enum in the NIHMS DTD
  • The mapping should be done in a configuration file. Should in the repositories.json or in the yaml file.
    • If only going to be used for the deposits, should only be in the respositories.json, but if this code could be something more than a deposit, then it should go into the policy object in the pass data model.
    • Note that if we end up putting these external funder identifiers on policy objects, since funder points to a policy there could be more than one funder using a given policy so we would need a list of identifiers on the policy object. (https://eclipse-pass.slack.com/archives/C035MNLRD44/p1704222666248669)

[tsande16]

All funders in PASS have an associated DOI from crossref. There is also a way to add funders in crossref using this form: https://support.crossref.org/hc/en-us/requests/new?ticket_form_id=360001642691

I downloaded the full CSV of all the funders and there is a total list of 43,288 funders in the Open Funder Registry.

List of all funders and the crossref DOI with an associated policy in PASS:

http://dx.doi.org/10.13039/100000054,"National Cancer Institute", 
http://dx.doi.org/10.13039/100000053,"National Eye Institute",
http://dx.doi.org/10.13039/100000050,"National Heart, Lung, and Blood Institute",
http://dx.doi.org/10.13039/100000051,"National Human Genome Research Institute",
http://dx.doi.org/10.13039/100000049,"National Institute on Aging", 
http://dx.doi.org/10.13039/100000027,"National Institute on Alcohol Abuse and Alcoholism",
http://dx.doi.org/10.13039/100000060,"National Institute of Allergy and Infectious Diseases",
http://dx.doi.org/10.13039/100000069,"National Institute of Arthritis and Musculoskeletal and Skin Diseases",
http://dx.doi.org/10.13039/100000070,"National Institute of Biomedical Imaging and Bioengineering",
http://dx.doi.org/10.13039/100009633,"Eunice Kennedy Shriver National Institute of Child Health and Human Development",
http://dx.doi.org/10.13039/100000055,"National Institute on Deafness and Other Communication Disorders", 
http://dx.doi.org/10.13039/100000072,"National Institute of Dental and Craniofacial Research",
http://dx.doi.org/10.13039/100000062,"National Institute of Diabetes and Digestive and Kidney Diseases", 
http://dx.doi.org/10.13039/100000026,"National Institute on Drug Abuse",
http://dx.doi.org/10.13039/100000066,"National Institute of Environmental Health Sciences", 
http://dx.doi.org/10.13039/100000057,"National Institute of General Medical Sciences", 
http://dx.doi.org/10.13039/100000025,"National Institute of Mental Health", 
http://dx.doi.org/10.13039/100000065,"National Institute of Neurological Disorders and Stroke",
http://dx.doi.org/10.13039/100000056,"National Institute of Nursing Research",
http://dx.doi.org/10.13039/100000092,"U.S. National Library of Medicine", 
http://dx.doi.org/10.13039/100000061,"Fogarty International Center", 
http://dx.doi.org/10.13039/100000002,"National Institutes of Health", 
http://dx.doi.org/10.13039/100006108,"National Center for Advancing Translational Sciences", 
http://dx.doi.org/10.13039/100000098,"NIH Clinical Center", 
http://dx.doi.org/10.13039/100006545,"National Institute on Minority Health and Health Disparities", 
http://dx.doi.org/10.13039/100000052,"NIH Office of the Director",
http://dx.doi.org/10.13039/100008460,"National Center for Complementary and Integrative Health",
http://dx.doi.org/10.13039/100021704,"Administration for Strategic Preparedness and Response",
http://dx.doi.org/10.13039/100000038,"U.S. Food and Drug Administration",
http://dx.doi.org/10.13039/100000133,"Agency for Healthcare Research and Quality", 
http://dx.doi.org/10.13039/100000030,"Centers for Disease Control and Prevention", 
http://dx.doi.org/10.13039/100000125,"National Institute for Occupational Safety and Health", 
http://dx.doi.org/10.13039/100000738,"U.S. Department of Veterans Affairs", 
http://dx.doi.org/10.13039/100000139,"U.S. Environmental Protection Agency", 
http://dx.doi.org/10.13039/100000011,"Howard Hughes Medical Institute"

[tsande16]

Crossref Open Funder Registry seems like a good resource to use for funder identifiers. There is a strong governance, and it is widely used by the academic community, not just for journals and publications, but also for funders and grants. Adopting the standardized identifiers for funders will make PASS more robust in uniquely identifying funders.

Board and Governance: https://www.crossref.org/board-and-governance/

Usage by other organizations:

https://direct.mit.edu/qss/article/1/1/414/15577/Crossref-The-sustainable-source-of-community-owned

"This paper describes the scholarly metadata collected and made available by Crossref, as well as its importance in the scholarly research ecosystem. Containing over 106 million records and expanding at an average rate of 11% a year, Crossrefs metadata has become one of the major sources of scholarly data for publishers, authors, librarians, funders, and researchers. The metadata set consists of 13 content types, including not only traditional types, such as journals and conference papers, but also data sets, reports, preprints, peer reviews, and grants. The metadata is not limited to basic publication metadata, but can also include abstracts and links to full text, funding and license information, citation links, and the information about corrections, updates, retractions, etc. This scale and breadth make Crossref a valuable source for research in scientometrics, including measuring the growth and impact of science and understanding new trends in scholarly communications. The metadata is available through a number of APIs, including REST API and OAI-PMH. In this paper, we describe the kind of metadata that Crossref provides and how it is collected and curated. We also look at Crossref’s role in the research ecosystem and trends in metadata curation over the years, including the evolution of its citation data provision. We summarize the research used in Crossref’s metadata and describe plans that will improve metadata quality and retrieval in the future."

Data from crossref about their growth of grants and relationships to those grants (publications, funders etc): https://www.crossref.org/blog/the-more-the-merrier-or-how-more-registered-grants-means-more-relationships-with-outputs/

• The overall numbers changed a lot between March 2022 and January 2023:

  • the total number of registered grants doubled (from ~38k to ~76k)
  • the total numbers of relationships established between grants and research outputs quadrupled (from 21k to 92k)
  • the percentage of linked grants increased substantially (from 10% to 23%)

• Most of this growth can be attributed to one funder, the European Union. They started registering grants with us in December 2022, and:

  • their grants constitute 47% of all grants registered by January 2023 and 95% of grants registered between March 2022 and January 2023
  • 72% of all established relationships involve their grants

[tsande16]

Outcome: Modifying the PASS data model, or introducing a new funder ID creates more complications and there are surrounding questions about how users of PASS would use this capability in terms of instantiating/mapping their funders.

Proposed solution: Our current solution is to use the localkey from the funder and created a mapping between that and the nomenclature that NIHMs uses in their DTD for federal agencies (nih, cdc, fda)

Future Considerations: Once we get more feedback from collaboraters/users of pass, we will want to revisit this solution and possibly put in place a more robust identifier for funders.