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The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization

Mullen, Kathleen (ORCID:0000000250028648)·Tammen, Imke (ORCID:0000000255206597)·Matentzoglu, Nicolas (ORCID:0000000273561779)·Mather, Marius (ORCID:0000000236166235)·Balhoff, James (ORCID:0000000286886599)·Esdaile, Elizabeth (ORCID:0000000162389793)·Leroy, Gregoire (ORCID:0000000325884431)·Park, Carissa (ORCID:0000000223465201)·Rando, Halie (ORCID:0000000176881770)·Saklou, Nadia (ORCID:0000000178943947)·Webb, Tracy (ORCID:0000000345473787)·Vasilevsky, Nicole (ORCID:0000000152083432)·Mungall, Christopher (ORCID:0000000266012165)·Haendel, Melissa (ORCID:0000000191148737)·Nicholas, Frank (ORCID:0000000291783965)·Toro, Sabrina (ORCID:0000000241427153)
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Abstract

Abstract Background Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in diagnostics, treatments, and precision medicine. Hypothesis/Objectives A single, coherent, logic-based standard for documenting breed names in health, production, and research-related records will improve data use capabilities in veterinary and comparative medicine. Animals No live animals were used. Methods The Vertebrate Breed Ontology (VBO) was created from breed names and related information compiled from the Food and Agriculture Organization of the United Nations, breed registries, communities, and experts, using manual and computational approaches. Each breed is represented by a VBO term that includes breed information and provenance as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence–readiness. Results VBO is an open, community-driven ontology representing over 19 500 livestock and companion animal breed concepts covering 49 species. Breeds are classified based on community and expert conventions (e.g., cattle breed) and supported by relations to the breed's genus and species indicated by National Center for Biotechnology Information (NCBI) Taxonomy terms. Relationships between VBO terms (e.g., relating breeds to their foundation stock) provide additional context to support advanced data analytics. VBO term metadata includes synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and Clinical Importance The adoption of VBO as a standard for breed names in databases and veterinary electronic health records enhances veterinary data interoperability and computability, supporting precision medicine.

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Mullen, Kathleen (ORCID:0000000250028648), Tammen, Imke (ORCID:0000000255206597), Matentzoglu, Nicolas (ORCID:0000000273561779), Mather, Marius (ORCID:0000000236166235), Balhoff, James (ORCID:0000000286886599), Esdaile, Elizabeth (ORCID:0000000162389793), Leroy, Gregoire (ORCID:0000000325884431), Park, Carissa (ORCID:0000000223465201), Rando, Halie (ORCID:0000000176881770), Saklou, Nadia (ORCID:0000000178943947), Webb, Tracy (ORCID:0000000345473787), Vasilevsky, Nicole (ORCID:0000000152083432), Mungall, Christopher (ORCID:0000000266012165), Haendel, Melissa (ORCID:0000000191148737), Nicholas, Frank (ORCID:0000000291783965), Toro, Sabrina (ORCID:0000000241427153). 2025-07-01. The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization. https://doi.org/10.1111/jvim.70133

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DOE OSTI2024

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DOE OSTI2024

The endocannabinoid system in bovine tissues: characterization of transcript abundance in the growing Holstein steer

Abstract Background The endocannabinoid system (ECS) is highly integrated with seemingly all physiological and pathophysiological processes in the body. There is increasing interest in utilizing bioactive plant compounds, for promoting health and improving production in livestock. Given the established interaction between phytochemicals and the ECS, there are many opportunities for identification and development of therapies to address a range of diseases and disorders. However, the ECS has not been thoroughly characterized in cattle, especially in the gastrointestinal tract. The objective of this study was to characterize the distribution and transcriptional abundance of genes associated with the endocannabinoid system in bovine tissues. Methods Tissues including brain, spleen, thyroid, lung, liver, kidney, mesenteric vein, tongue, sublingual mucosa, rumen, omasum, duodenum, jejunum, ileum and colon were collected from 10-mo old Holstein steers (n = 6). Total RNA was extracted and gene expression was measured using absolute quantification real time qPCR. Gene expression of endocannabinoid receptorsCNR1andCNR2, synthesis enzymesDAGLA,DAGLBandNAPEPLD, degradation enzymesMGLLandFAAH, and transient receptor potential vanilloidsTRPV3andTRPV6was measured. Data were analyzed in R using a Kruskal-Wallis followed by a Wilcoxon rank-sum test. Results are reported as the median copy number/20 ng of equivalent cDNA (CN) with interquartile range (IQR). Results The greatest expression ofCNR1andCNR2was in the brain and spleen, respectively. Expression of either receptor was not detected in any gastrointestinal tissues, however there was a tendency (P = 0.095) forCNR2to be expressed above background in rumen. Expression of endocannabinoid synthesis and degradation enzymes varied greatly across tissues. Brain tissue had the greatestDAGLAexpression at 641 CN (IQR 52;P ≤ 0.05).DAGLBwas detected in all tissues, with brain and spleen having the greatest expression (P ≤ 0.05). Expression ofNAPEPLDin the gastrointestinal tract was lowest in tongue and sublingual mucosal. There was no difference in expression ofNAPEPLDbetween hindgut tissues, however these tissues collectively had 592% greater expression than rumen and omasum (P ≤ 0.05). WhileMGLLwas found to be expressed in all tissues, expression ofFAAHwas only above the limit of detection in brain, liver, kidney, jejunum and ileum.TRPV3was expressed above background in tongue, rumen, omasum and colon. Although not different from each other, thyroid and duodenum had the greatest expression ofTRPV6, with 285 (IQR 164) and 563 (IQR 467) CN compared to all other tissues (P < 0.05). Conclusions These data demonstrate the complex distribution and variation of the ECS in bovine tissues. Expression patterns suggest that regulatory functions of this system are tissue dependent, providing initial insight into potential target tissues for manipulation of the ECS.

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