{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:15:58Z","timestamp":1753884958425},"reference-count":10,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a \u201crealizable concretization\u201d (RC), is realized. This representation, which we call the \u201cRC-account\u201d, provides a straightforward way to relate a plan specification to the entity that bears the realizable concretization and the process that realizes the realizable concretization. However, the adequacy of the RC-account has not been evaluated in the scientific literature. In this manuscript, we provide this evaluation and, thereby, give ontology developers sound reasons to use or not use the RC-account pattern.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Analysis of the RC-account reveals that it is not adequate for representing failed plans. If the realizable concretization is flawed in some way, it is unclear what (if any) relation holds between the realizable entity and the plan specification. If the execution (i.e., realization) of the realizable concretization fails to carry out the actions given in the plan specification, it is unclear under the RC-account how to directly relate the failed execution to the entity carrying out the instructions given in the plan specification. These issues are exacerbated in the presence of changing plans.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We propose two solutions for representing failed plans. The first uses the Common Core Ontologies \u2018prescribed by\u2019 relation to connect a plan specification to the entity or process that utilizes the plan specification as a guide. The second, more complex, solution incorporates the process of creating a plan (in the sense of an intention to execute a plan specification) into the representation of executing plan specifications. We hypothesize that the first solution (i.e., use of \u2018prescribed by\u2019) is adequate for most situations. However, more research is needed to test this hypothesis as well as explore the other solutions presented in this manuscript.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13326-024-00315-0","type":"journal-article","created":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T23:02:37Z","timestamp":1724108557000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Concretizing plan specifications as realizables within the OBO foundry"],"prefix":"10.1186","volume":"15","author":[{"given":"William D.","family":"Duncan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Diller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damion","family":"Dooley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William R.","family":"Hogan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Beverley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,8,20]]},"reference":[{"key":"315_CR1","unstructured":"Rudnicki R. An overview of the common core ontologies. CUBRC Inc, p. 27, 2019."},{"key":"315_CR2","unstructured":"Smith B, Ceusters W. Aboutness: Towards foundations for the information artifact ontology, in CEUR Workshop Proceedings, 2015, pp. 1\u20135. [Online]. Available: https:\/\/ceur-ws.org\/Vol-1515\/regular10.pdf."},{"key":"315_CR3","doi-asserted-by":"crossref","unstructured":"Arp R, Smith B, Spear AD. Building ontologies with basic formal ontology. MIT Press; 2015.","DOI":"10.7551\/mitpress\/9780262527811.001.0001"},{"key":"315_CR4","doi-asserted-by":"crossref","unstructured":"Jackson R et al. OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies, Database, vol. 2021, Oct. 2021.","DOI":"10.1093\/database\/baab069"},{"issue":"4","key":"315_CR5","doi-asserted-by":"publisher","first-page":"e0154556","DOI":"10.1371\/journal.pone.0154556","volume":"11","author":"A Bandrowski","year":"2016","unstructured":"Bandrowski A, et al. The Ontology for Biomedical investigations. PLoS ONE. 2016;11(4):e0154556. https:\/\/doi.org\/10.1371\/journal.pone.0154556.","journal-title":"PLoS ONE"},{"key":"315_CR6","unstructured":"Hitzler P, Kr\u00f6tzsch M. OWL 2 Web Ontology Language Primer, W3C Recommendation, 11 December 2012."},{"key":"315_CR7","unstructured":"Horridge M. The Manchester OWL Syntax, In OWLed. Vol. 216. 2006."},{"key":"315_CR8","doi-asserted-by":"crossref","unstructured":"Otte JN, Beverley J, Ruttenberg A. BFO: Basic formal ontology, Appl. Ontol., vol. 17, no. 1, pp. 17\u201343, 2022.","DOI":"10.3233\/AO-220262"},{"key":"315_CR9","unstructured":"Overton J et al. Sep., COB: A Core Ontology for Biology and Biomedicine, in The first FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI-22) at the ICBO 2022: International Conference on Biomedical Ontology, Ann Arbor, MI, 2022."},{"key":"315_CR10","unstructured":"Barton A, Vieu L, L. and, Ethier JF. Directing actions, Workshop on Foundational Ontology (FOUST III), Joint Ontology Workshops (JOWO 2019), CEUR Workshop Proceedings, 2019."}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-024-00315-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-024-00315-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-024-00315-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T23:02:41Z","timestamp":1724108561000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/s13326-024-00315-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,20]]},"references-count":10,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["315"],"URL":"https:\/\/doi.org\/10.1186\/s13326-024-00315-0","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,20]]},"assertion":[{"value":"18 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"15"}}