From e55a835107845a0c31e4723311fe9ffb36505cca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ra=C3=BAl=20Ortega?= Date: Tue, 19 Sep 2023 10:44:12 +0200 Subject: [PATCH 1/4] Update ontoavida.md Whe have added an usage and the link to a paper describing ontoavida that has recently been published --- ontology/ontoavida.md | 28 ++++++++++++++++++++++++---- 1 file changed, 24 insertions(+), 4 deletions(-) diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index 7c8fb4441..e5eddbe8d 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -2,9 +2,13 @@ layout: ontology_detail id: ontoavida title: 'OntoAvida: ontology for Avida digital evolution platform' +browsers: +- title: Ontoavida HTML Browser + label: Human-readable (HTML) + url: https://owl.fortunalab.org/ontoavida/ contact: email: fortuna@ebd.csic.es - github: miguelfortuna + github: fortunalab label: Miguel A. Fortuna orcid: 0000-0002-8374-1941 dependencies: @@ -21,13 +25,29 @@ license: url: https://creativecommons.org/licenses/by/4.0/ preferredPrefix: ONTOAVIDA products: -- id: ontoavida.owl -- id: ontoavida.obo + - id: ontoavida.owl + title: OWL + description: The main ontology in OWL + page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.owl + - id: ontoavida.obo + title: OBO + description: Equivalent to ontoavida.owl, in obo format + page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo + +publications: + - id: https://doi.org/10.1038/s41597-023-02514-3 + title: "Ontology for the Avida digital evolution platform" repository: https://gitlab.com/fortunalab/ontoavida tags: - digital evolution - artificial life tracker: https://gitlab.com/fortunalab/ontoavida/-/issues activity_status: active +usages: + - user: https://cran.r-project.org/package=avidaR + description: An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms + examples: + - url: http://doi.org/10.7717/peerj-cs.1568 + description: "avidaR: an R library to perform complex queries on an ontology-based database of digital organisms" --- -The **Ontology for Avida ([OntoAvida](https://gitlab.com/fortunalab/ontoavida))** project aims to develop an integrated vocabulary for the description of [Avida](https://github.com/devosoft/avida), the most widely used computational approach for performing experimental evolution. The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. In addition, OntoAvida will allow researchers to make inference (e.g., on phenotypic plasticity) based on certain rules and constraints, facilitate the reproducibility of the *in silico* evolution experiments reported in the [scientific literature](https://gitlab.com/fortunalab/ontoavida#references), and trace the provenance of the data stored in AvidaDB, a semantic database that stores genomes and transcriptomes of more than a million digital organisms. +The **Ontology for Avida ([OntoAvida](https://owl.fortunalab.org/ontoavida/))** aims to develop an integrated vocabulary for the description of [Avida](https://github.com/devosoft/avida), the most widely used computational approach for performing experimental evolution using digital organisms–self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of [in silico evolution experiments](https://gitlab.com/fortunalab/ontoavida#references) and trace the provenance of the data stored in avidaDB–an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms. From 06489b104481336042b8a2b8437e05da93ee0790 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ra=C3=BAl=20Ortega?= Date: Tue, 19 Sep 2023 10:52:32 +0200 Subject: [PATCH 2/4] trailing space removed --- ontology/ontoavida.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index e5eddbe8d..575fc2d05 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -35,7 +35,7 @@ products: page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo publications: - - id: https://doi.org/10.1038/s41597-023-02514-3 + - id: https://doi.org/10.1038/s41597-023-02514-3 title: "Ontology for the Avida digital evolution platform" repository: https://gitlab.com/fortunalab/ontoavida tags: From ef47cb809480dae4ac7029ed8069c76e08d80682 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ra=C3=BAl=20Ortega?= Date: Tue, 19 Sep 2023 11:00:46 +0200 Subject: [PATCH 3/4] tox -e lint --- ontology/ontoavida.md | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index 575fc2d05..a2d8cce26 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -25,29 +25,28 @@ license: url: https://creativecommons.org/licenses/by/4.0/ preferredPrefix: ONTOAVIDA products: - - id: ontoavida.owl - title: OWL - description: The main ontology in OWL - page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.owl - - id: ontoavida.obo - title: OBO - description: Equivalent to ontoavida.owl, in obo format - page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo - +- id: ontoavida.owl + title: OWL + description: The main ontology in OWL + page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.owl +- id: ontoavida.obo + title: OBO + description: Equivalent to ontoavida.owl, in obo format + page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo publications: - - id: https://doi.org/10.1038/s41597-023-02514-3 - title: "Ontology for the Avida digital evolution platform" +- id: https://doi.org/10.1038/s41597-023-02514-3 + title: Ontology for the Avida digital evolution platform repository: https://gitlab.com/fortunalab/ontoavida tags: - digital evolution - artificial life tracker: https://gitlab.com/fortunalab/ontoavida/-/issues -activity_status: active usages: - - user: https://cran.r-project.org/package=avidaR - description: An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms - examples: - - url: http://doi.org/10.7717/peerj-cs.1568 - description: "avidaR: an R library to perform complex queries on an ontology-based database of digital organisms" +- description: An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms + examples: + - description: 'avidaR: an R library to perform complex queries on an ontology-based database of digital organisms' + url: http://doi.org/10.7717/peerj-cs.1568 + user: https://cran.r-project.org/package=avidaR +activity_status: active --- The **Ontology for Avida ([OntoAvida](https://owl.fortunalab.org/ontoavida/))** aims to develop an integrated vocabulary for the description of [Avida](https://github.com/devosoft/avida), the most widely used computational approach for performing experimental evolution using digital organisms–self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of [in silico evolution experiments](https://gitlab.com/fortunalab/ontoavida#references) and trace the provenance of the data stored in avidaDB–an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms. From 207807e191728bf3788772f6abcd1ed1b89d9d0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ra=C3=BAl=20Ortega?= Date: Mon, 25 Sep 2023 09:49:21 +0200 Subject: [PATCH 4/4] Update ontoavida.md --- ontology/ontoavida.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index a2d8cce26..9bce4435d 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -8,7 +8,7 @@ browsers: url: https://owl.fortunalab.org/ontoavida/ contact: email: fortuna@ebd.csic.es - github: fortunalab + github: miguelfortuna label: Miguel A. Fortuna orcid: 0000-0002-8374-1941 dependencies: