Mining Rare Associations between Biological OntologiesMining Rare Associations between Biological Ontologies

In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology ... Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The ... We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. ... association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or ...
more infohttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084475

Biological Collections Ontology - protein - Classes | NCBO BioPortalBiological Collections Ontology - protein - Classes | NCBO BioPortal

Ontology of Biological and Clinical Statistics LOOM http://purl.obolibrary.org/obo/PR_000000001 Ontology of Biological and ... Chemical Entities of Biological Interest Ontology LOOM http://purl.obolibrary.org/obo/CHEBI_36080 Ontology of Biological ... www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#Protein Cell Line Ontology [by Mahadevan] LOOM ... www.imgt.org/download/IMGT-ONTOLOGY/IMGT-ONTOLOGY-v1-0-2.owl#protein Immunogenetics Ontology LOOM ...
more infohttp://bioportal.bioontology.org/ontologies/BCO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPR_000000001

Genotype Ontology - biological process - Classes | NCBO BioPortalGenotype Ontology - biological process - Classes | NCBO BioPortal

http://purl.obolibrary.org/obo/ODGI.owl#Biological_Process OGDI LOOM http://www.semanticweb.org/ontologies/2010/5/22/ ... http://www.co-ode.org/ontologies/galen#BiologicalProcess GALEN LOOM http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_ ... http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Biological_process GFO-BIO LOOM ... The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ...
more infohttp://bioportal.bioontology.org/ontologies/GENO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGENO_0000351

Program in Detail | International Conference on Biological Ontology 2018Program in Detail | International Conference on Biological Ontology 2018

Ontology 101 (Part-I): A how-to guide to create, manage, and release an OBO ontology. Organizers: Nicole Vasilevsky, James A. ... Ontology 101 (Part-II): A how-to guide to create, manage, and release an OBO ontology. Organizers: Nicole Vasilevsky, James A. ... Phenotype Ontology workshop report (Phenotype Ontology Group) -15 minutes. *Flash Talks (Posters and Demo) - PART I. Posters ... Phenotype Ontologies Traversing All The Organisms (POTATO) (Session-2). Aligning phenotype ontologies using design patterns. ...
more infohttp://icbo2018.cgrb.oregonstate.edu/program

Abstracts | International Conference on Biological Ontology 2018Abstracts | International Conference on Biological Ontology 2018

Multi-species Malformation Ontologies", in International Conference on Biomedical Ontology (ICBO 2018), 2018.*BibTex ...
more infohttp://icbo2018.cgrb.oregonstate.edu/abstracts?f%5Bkeyword%5D=113&s=author&o=asc

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related...Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related...

Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry ... we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and ... These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to ... We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of ...
more infohttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089606

Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in...Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in...

Gene Ontology (GO) provides a valuable source of knowledge for model training and validation. The increasing collection of ... The results showed that, of the 148 pursued GO biological processes, fifteen terms each had at least one model with FDR- ... Furthermore, we observed that the memberships of the genes involved in all the three pursued children biological processes on ... This study focused on using support vector machines (SVM) to predict GO biological processes from individual or multiple-tissue ...
more infohttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-129

IT505: Towards a Standard Ontology Metadata Model | International Conference on Biological Ontology & BioCreativeIT505: Towards a Standard Ontology Metadata Model | International Conference on Biological Ontology & BioCreative

Due to the large number of emerging bio-ontologies, it is challenging for ontology for their applications. Therefore, it is ... Bio-ontologies are becoming increasingly important in semantic alignment for data integration, information exchange, and ... important to have a consistent terminology metadata model and a resource for discovering appropriate ontologies or other ...
more infohttp://icbo2016.cgrb.oregonstate.edu/node/311

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related...Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related...

Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry ... we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and ... An Introduction to the Biological Collections Ontology and Related Ontologies. ... "Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related ...
more infohttps://kuscholarworks.ku.edu/handle/1808/13473

Analysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic CancerAnalysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic Cancer

... Hang Yin,1 ShaoPeng Wang,2 Yu- ... M. A. Harris, J. I. Deegan, J. Lomax et al., "The gene ontology project in 2008," Nucleic Acids Research, vol. 36, pp. D440- ... L. Chen, C. Chu, J. Lu, X. Kong, T. Huang, and Y.-D. Cai, "Gene ontology and KEGG pathway enrichment analysis of a drug target- ... J. Yang, L. Chen, X. Kong, T. Huang, and Y.-D. Cai, "Analysis of tumor suppressor genes based on gene ontology and the KEGG ...
more infohttps://www.hindawi.com/journals/bmri/2016/7861274/ref/

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.  - PubMed - NCBIBiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. - PubMed - NCBI

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are ... BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.. Maere S1, Heymans K ... BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/15972284?dopt=Abstract

BIT104: Cardiovascular Health and Physical Activity: A Model for Health Promotion and Decision Support Ontologies |...BIT104: Cardiovascular Health and Physical Activity: A Model for Health Promotion and Decision Support Ontologies |...

International Conference on Biological Ontology & BioCreative August 1-4, 2016, Corvallis, Oregon, USA ... These conceptual maps lay the foundation for accelerated creation of health-focused ontologies, which ultimately equip DSS with ... BIT104: Cardiovascular Health and Physical Activity: A Model for Health Promotion and Decision Support Ontologies ... Advancement of health science depends on timely development and implementation of health (rather than disease) ontologies. We ...
more infohttp://icbo2016.cgrb.oregonstate.edu/node/249

Gene ontology biological process terms.Direction of the | Open-iGene ontology biological process terms.Direction of the | Open-i

Gene ontology biological process terms.Direction of the impact of GO Biological process terms with the largest difference in ... pone.0137644.g005: Gene ontology biological process terms.Direction of the impact of GO Biological process terms with the ... pone.0137644.g005: Gene ontology biological process terms.Direction of the impact of GO Biological process terms with the ... Mentions: In Fig 5 is reported the direction of the impact of the GO Biological processes (calculated by DIA) with the largest ...
more infohttps://openi.nlm.nih.gov/detailedresult.php?img=PMC4580618_pone.0137644.g005&req=4

Biological Collections Ontology - entity - Classes | IBC AgroPortalBiological Collections Ontology - entity - Classes | IBC AgroPortal

Plant Experimental Conditions Ontology LOOM http://purl.obolibrary.org/obo/BFO_0000001 Plant Experimental Conditions Ontology ... http://purl.bioontology.org/ontology/STY/T071 UMLS Semantic Network LOOM Interportal mappings. Delete. Mapping To. Ontology. ... To see all of the ontologies in AgroPortal visit the full site. ... Ontology. Source. Relations. There are currently no external ... Sustainable Development Goals Interface Ontology LOOM http://purl.obolibrary.org/obo/BFO_0000001 Sustainable Development Goals ...
more infohttp://obo-foundry.agroportal.lirmm.fr/ontologies/BCO?p=classes

Biological Collections Ontology - continuant - Classes | NCBO BioPortalBiological Collections Ontology - continuant - Classes | NCBO BioPortal

The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by ... http://www.owl-ontologies.com/Ontology1435740495.owl#Continuant OF LOOM http://purl.obolibrary.org/obo/bfo#Continuant PDO_CAS ... http://bioontology.org/projects/ontologies/birnlex#Continuant BIRNLEX LOOM http://www.ifomis.org/bfo/1.1/snap#Continuant FLU ...
more infohttps://ctsa-hom.bioportal.bioontology.org/ontologies/BCO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000002

Zebrafish Phenotype Ontology - biological process - Classes | NCBO BioPortalZebrafish Phenotype Ontology - biological process - Classes | NCBO BioPortal

Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division ... Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division ...
more infohttp://obo-foundry.bioportal.bioontology.org/ontologies/ZP?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0008150

Cellular microscopy phenotype ontology - biological process - Classes | NCBO BioPortalCellular microscopy phenotype ontology - biological process - Classes | NCBO BioPortal

Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the ... http://purl.obolibrary.org/obo/ODGI.owl#Biological_Process OGDI LOOM http://www.semanticweb.org/ontologies/2010/5/22/ ... http://www.co-ode.org/ontologies/galen#BiologicalProcess GALEN LOOM http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_ ...
more infohttp://obo-foundry.bioportal.bioontology.org/ontologies/CMPO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0008150

Translation: Simondon, Completion of Section I, Chapter 1, The Individual and Its Physico-Biological Genesis - Fractal OntologyTranslation: Simondon, Completion of Section I, Chapter 1, The Individual and Its Physico-Biological Genesis - Fractal Ontology

Pingback: Translation: Simondon and the Physico-Biological Genesis of the Individual « Fractal Ontology ... Fractal Ontology. refracting theory: politics, cybernetics, philosophy. Translation: Simondon, Completion of Section I, Chapter ... It is also not enough to suppose in the knowledge that one takes from the technical operation a paradigm initially biological: ... The internal and external, depth and height, have biological value only through this topological surface of contact. Thus, even ...
more infohttps://fractalontology.wordpress.com/2007/10/19/translation-simondon-completion-of-section-i-chapter-1-the-individual-and-its-physico-biological-genesis/

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis | Journal of...The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis | Journal of...

The Ontology of Biological and Clinical Statistics (OBCS) is a community-based open source ontology in the domain of biological ... and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ... The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. The terms ... We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how ...
more infohttps://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0100-2

The environment ontology: contextualising biological and biomedical entities | Journal of Biomedical Semantics | Full TextThe environment ontology: contextualising biological and biomedical entities | Journal of Biomedical Semantics | Full Text

... open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science ... to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper ... The ontology is available from http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching ... As biological and biomedical research increasingly reference the environmental context of the biological entities under study, ...
more infohttps://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-43

PENN S TATE Compatible text, visual and mathematical representations for biological process ontologies Nigam Shah Penn State...PENN S TATE Compatible text, visual and mathematical representations for biological process ontologies Nigam Shah Penn State...

Protein P induces transcription of gene X We define an event as a relationship between two biological entities, which we call ... PENN S TATE Hypotheses and Events An hypothesis about a biological process is a statement about relationships within a ... 2 PENN S TATE Ontologies in Molecular Biology An ontology is a formal way of representing knowledge. -In an ontology, concepts ... 1 PENN S TATE Compatible text, visual and mathematical representations for biological process ontologies Nigam Shah Penn State ...
more infohttp://slideplayer.com/slide/797224/

Open Biomedical Ontologies / Mailing ListsOpen Biomedical Ontologies / Mailing Lists

obo-discuss - General discussion list for the open biological ontologies project You can subscribe to this list here. ... Reasoning with biomedical ontologies • Evaluation of biomedical ontologies • Biomedical ontology and the Semantic Web * * * ... Principles-based ontologies are being developed for the description of biological and biomedical phenomena of almost every type ... To be maximally effective, such ontologies must work well together. But as ontologies become more commonly used and as their ...
more infohttps://sourceforge.net/p/obo/mailman/obo-discuss/?viewmonth=201102

Integrating phenotype ontologies across multiple species | Genome Biology | Full TextIntegrating phenotype ontologies across multiple species | Genome Biology | Full Text

Chemical Entities of Biological Interest (CHEBI) is an ontology of chemical entities [13]. The OBO Protein ontology (PRO) [14] ... Open biological ontologies. Ontologies consist of collections of classes, arranged in a relational graph, to provide a ... using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. ... the Mammalian Phenotype ontology (MP) [15]; the Worm Phenotype ontology (WP); the Plant Trait ontology (TO) [16]; the Human ...
more infohttps://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-1-r2

Measuring phenotype-phenotype similarity through the interactome | BMC Bioinformatics | Full TextMeasuring phenotype-phenotype similarity through the interactome | BMC Bioinformatics | Full Text

PhenoNet was evaluated on two independent evaluation datasets: gene ontology and gene expression data. The result shows that ... Selected articles from the Biological Ontologies and Knowledge bases workshop 2017. The full contents of the supplement are ... ontology-based method [29] and Menches method [20]. Ontology-based method calculated the phenotype similarity based on the IC ... Specifically, given a biological network N(V,E), a phenotype p and a set of proteins G p related to p, the network module of p ...
more infohttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2102-9