Standards

Figure 1 – FAIRSCAPE processes and packages multi-modal lab and integration pipeline data with
rich descriptive metadata serialized in JSON-LD with Schema.org vocabulary, deep provenance graphs, and extended AI-readiness datasheets.  Data is then pushed to the UVA instance of Dataverse, a long-term sustainable, NIH-validated GREI repository, through its REST API.

FAIRSCAPE consists of client and server components that manage data releases and provide rich metadata on datasets from the CM4AI Data Acquisition, Tools, and Standards groups. These metadata include persistent FAIR identifiers; descriptive metadata using the schema.org vocabulary; metadata criteria for validating AI-readiness including comprehensive datasheets with semantic, statistical, provenance, ethical, and usability characterization of the released datasets. Metadata are provided in both human- and machine-readable form. 

Provenance is tracked using the Evidence Graph Ontology (EVI), an extension of W3C PROV. Resolvable provenance records in JSON-LD graph language are provided on the data, software, and computations in this project, to support fully informed data and software reuse. CM4AI Standards plays a central role, in close collaboration with the Data Acquisition and Tools modules, in providing the foundation for reliable AI reuse of all CM4AI data and software products, and for enabling Common Metadata packaging across the Bridge2AI program, and integration with the Common Fund Data Ecosystem, in collaboration with the other Bridge2AI Grand Challenges (GCs).  

The CM4AI Standards co-PI has co-chaired the overall Bridge2AI Standards Working group since January 2024, with responsibility for ensuring significant GC input to key standards development activities, including the development of program-wide AI-Readiness criteria, in collaboration with the other GC Standards leads and the CM4AI Program Manager.

Select Publications

1.   Al Manir S, Niestroy J, Levinson MA, Clark T. Evidence Graphs: Supporting Transparent and FAIR Computation, with Defeasible Reasoning on Data, Methods, and Results. In: Glavic B, Braganholo V, Koop D, editors. Provenance and Annotation of Data and Processes [Internet]. Cham: Springer International Publishing; 2021 [cited 2022 Mar 16]. p. 39–50. Available from: https://link.springer.com/10.1007/978-3-030-80960-7_3
2.   Al Manir S, Niestroy J, Levinson M, Clark T. EVI: The Evidence Graph Ontology, OWL 2 Vocabulary [Internet]. Zenodo; 2021. Available from: https://doi.org/10.5281/zenodo.4630931
3.   Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines [Internet]. 2024 [cited 2024 Sep 27]. Available from: http://biorxiv.org/lookup/doi/10.1101/2024.05.21.589311
4.   Clark T, Caufield H, Parker JA, Al Manir S, Amorim E, Eddy J, Gim N, Gow B, Goar W, Haendel M, Hansen JN, Harris N, Hermjakob H, Joachimiak M, Jordan G, Lee IH, McWeeney SK, Nebeker C, Nikolov M, Shaffer J, Sheffield N, Sheynkman G, Stevenson J, Chen JY, Mungall C, Wagner A, Kong SW, Ghosh SS, Patel B, Williams A, Munoz-Torres MC. AI-readiness for Biomedical Data: Bridge2AI Recommendations. bioRxiv. 2024 Nov 24;2024.10.23.619844. PMCID: PMC11526931
5.   Al Manir S, Levinson MA, Niestroy J, Churas C, Parker JA, Clark T. FAIRSCAPE: An Evolving AI-readiness Framework for Biomedical Research. BioRXiv [Internet]. 2024 Dec 23;2024.10.23.619844. Available from: https://www.biorxiv.org/content/10.1101/2024.10.23.619844v4
6.   Niestroy J. fairscape-cli 1.0.2 [Internet]. PYPI.org; 2024. Available from: https://pypi.org/project/fairscape-cli/
7.   Levinson MA, Al Manir S, Clark T. fairscape-cli: A utility for packaging objects and validating metadata for FAIRSCAPE. [Internet]. Zenodo; 2024 [cited 2024 Nov 27]. Available from: https://zenodo.org/doi/10.5281/zenodo.14014297
8.   Levinson MA, Niestroy J, Al Manir S, Clark T. FAIRSCAPE Server [Internet]. Zenodo; 2024 [cited 2024 Nov 27]. Available from: https://zenodo.org/doi/10.5281/zenodo.8136000
9.   Clark T, Parker J, Al Manir S, Axelsson U, Ballllosero Navarro F, Chinn B, Churas CP, Dailamy A, Doctor Y, Fall J, Forget A, Gao J, Hansen JN, Hu M, Johannesson A, Khaliq H, Lee YH, Lenkiewicz J, Levinson MA, Marquez C, Metallo C, Muralidharan M, Nourreddine S, Niestroy J, Obernier K, Pan E, Polacco B, Pratt D, Qian G, Schaffer L, Sigaeva A, Thaker S, Zhang Y, Bélisle-Pipon JC, Brandt C, Chen JY, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Idkeker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines – Data Release (0.6 Beta) [Internet]. University of Virginia Dataverse; 2025. Available from: https://doi.org/10.18130/V3/B35XWX
10.  Lenkiewicz J, Churas C, Hu M, Qian G, Jain M, Levinson MA, Manir SA, Qin Y, Fong D, Ono K, Gao C, Pratt D, Parker JA, Clark T, Ideker T, Schaffer LV. Cell mapping toolkit:An end-to-end pipeline for mapping subcellular organization. Bioinformatics. In Press;