From 1ab4bd68c8d50e37780123341bff4d19adcf53e1 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Wed, 2 Apr 2025 23:05:26 +0200 Subject: [PATCH 01/13] Create bmont.md bmont.md file added for the new accepted BMONT (Biomarker Ontology) --- ontology/bmont.md | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 ontology/bmont.md diff --git a/ontology/bmont.md b/ontology/bmont.md new file mode 100644 index 000000000..a8ee7388c --- /dev/null +++ b/ontology/bmont.md @@ -0,0 +1,41 @@ +--- +layout: ontology_detail +id: bmont +title: Biomarker Ontology +browsers: +- title: BioPortal Ontology Browser + label: BioPortal + url: https://bioportal.bioontology.org/ontologies/BMONT +contact: + email: alpha.tom.kodamullil@scai.fraunhofer.de + github: akodamullil + label: Alpha Tom Kodamullil + orcid: 0000-0001-9896-3531 +description: An ontology of biomarkers in medical and biological domains +domain: biomarker +homepage: https://github.com/SCAI-BIO/BiomarkerOntology +in_foundry_order: +license: + label: CC-BY 4.0 + url: http://creativecommons.org/licenses/by/4.0/ +preferredPrefix: BMONT +products: +- id: bmont.owl +- id: bmont.obo +publications: +- id: + title: +repository: https://github.com/SCAI-BIO/BiomarkerOntology +tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues +usages: +- description: The ontology is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM). + examples: + - description: + url: + publications: + - id: + title: + type: + user: +activity_status: active +--- From 0de1de261004b425b416da1b32ee9c22832e5376 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Wed, 2 Apr 2025 23:24:50 +0200 Subject: [PATCH 02/13] Update bmont.md bmont.md information update based on the https://github.com/OBOFoundry/obo-nor.github.io/blob/master/dashboard-config.yml --- ontology/bmont.md | 55 ++++++++++++++--------------------------------- 1 file changed, 16 insertions(+), 39 deletions(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index a8ee7388c..3a29a2e75 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -1,41 +1,18 @@ --- -layout: ontology_detail id: bmont -title: Biomarker Ontology -browsers: -- title: BioPortal Ontology Browser - label: BioPortal - url: https://bioportal.bioontology.org/ontologies/BMONT -contact: - email: alpha.tom.kodamullil@scai.fraunhofer.de - github: akodamullil - label: Alpha Tom Kodamullil - orcid: 0000-0001-9896-3531 -description: An ontology of biomarkers in medical and biological domains -domain: biomarker -homepage: https://github.com/SCAI-BIO/BiomarkerOntology -in_foundry_order: -license: - label: CC-BY 4.0 - url: http://creativecommons.org/licenses/by/4.0/ -preferredPrefix: BMONT -products: -- id: bmont.owl -- id: bmont.obo -publications: -- id: - title: -repository: https://github.com/SCAI-BIO/BiomarkerOntology -tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues -usages: -- description: The ontology is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM). - examples: - - description: - url: - publications: - - id: - title: - type: - user: -activity_status: active ---- + mirror_from: https://raw.githubusercontent.com/SCAI-BIO/BiomarkerOntology/main/BMONT-merged.owl + title: "Biomarker Ontology" + contact: + email: alpha.tom.kodamullil@scai.fraunhofer.de + label: Alpha Tom Kodamullil + orcid: 0000-0001-9896-3531 + github: akodamullil + description: The Biomarker Ontolody comprises a comprehensive knowledge involving a variety of fields of medical and biological aspects. + domain: health + homepage: https://github.com/SCAI-BIO/BiomarkerOntology + products: + - id: BMONT-merged.owl + tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues + license: + url: https://creativecommons.org/licenses/by/4.0/ + label: CC BY 4.0 From cfc2f88217b148a5547fb478f4f04a8fb69f33bd Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Mon, 14 Apr 2025 23:53:48 +0200 Subject: [PATCH 03/13] Update bmont.md Update after the review --- ontology/bmont.md | 58 ++++++++++++++++++++++++++++++++++------------- 1 file changed, 42 insertions(+), 16 deletions(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 3a29a2e75..74956c8a8 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -1,18 +1,44 @@ --- +layout: ontology_detail id: bmont - mirror_from: https://raw.githubusercontent.com/SCAI-BIO/BiomarkerOntology/main/BMONT-merged.owl - title: "Biomarker Ontology" - contact: - email: alpha.tom.kodamullil@scai.fraunhofer.de - label: Alpha Tom Kodamullil - orcid: 0000-0001-9896-3531 - github: akodamullil - description: The Biomarker Ontolody comprises a comprehensive knowledge involving a variety of fields of medical and biological aspects. - domain: health - homepage: https://github.com/SCAI-BIO/BiomarkerOntology - products: - - id: BMONT-merged.owl - tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues - license: - url: https://creativecommons.org/licenses/by/4.0/ - label: CC BY 4.0 +title: Biomarker Ontology +browsers: +- title: BioPortal Ontology Browser + label: BioPortal + url: [https://bioportal.bioontology.org/ontologies/BMONT] +contact: + email: alpha.tom.kodamullil@scai.fraunhofer.de + github: akodamullil + label: Alpha Tom Kodamullil + orcid: 0000-0001-9896-3531 +description: An ontology of phenotypic qualities (properties, attributes or characteristics) +domain: health +homepage: https://github.com/SCAI-BIO/BiomarkerOntology +in_foundry_order: +license: + label: CC BY 4.0 + url: http://creativecommons.org/licenses/by/4.0/ +preferredPrefix: BMONT +products: +- id: BMONT.owl +- id: bmont.obo + description: Includes axioms linking to other ontologies, but no imports of those ontologies +publications: +- id: + title: +- id: + title: Using ontologies to describe mouse phenotypes +repository: https://github.com/pato-ontology/pato +tracker: https://github.com/pato-ontology/pato/issues +usages: +- description: PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration. + examples: + - description: An abnormality in a cellular process. + url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213 + title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources + type: annotation + user: https://hpo.jax.org/app/ +activity_status: active +--- From 8105bed0cdca9898df7b5504dbac3b9f4e11b250 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Tue, 15 Apr 2025 00:03:56 +0200 Subject: [PATCH 04/13] Update bmont.md Modifications after the review --- ontology/bmont.md | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 74956c8a8..f9489512d 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -11,7 +11,7 @@ contact: github: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 -description: An ontology of phenotypic qualities (properties, attributes or characteristics) +description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects. domain: health homepage: https://github.com/SCAI-BIO/BiomarkerOntology in_foundry_order: @@ -28,17 +28,10 @@ publications: title: - id: title: Using ontologies to describe mouse phenotypes -repository: https://github.com/pato-ontology/pato -tracker: https://github.com/pato-ontology/pato/issues +repository: https://github.com/SCAI-BIO/BiomarkerOntology +tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue usages: -- description: PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration. - examples: - - description: An abnormality in a cellular process. - url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false - publications: - - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213 - title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources - type: annotation - user: https://hpo.jax.org/app/ +- description: BMONT is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM). + activity_status: active --- From 44766437f92a9d5370fee0d2d4186e6844d90057 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Thu, 24 Apr 2025 10:24:55 +0200 Subject: [PATCH 05/13] Update ontology/bmont.md Co-authored-by: Deepak --- ontology/bmont.md | 1 + 1 file changed, 1 insertion(+) diff --git a/ontology/bmont.md b/ontology/bmont.md index f9489512d..d1a21a857 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -1,5 +1,6 @@ --- layout: ontology_detail +layout: ontology_detail id: bmont title: Biomarker Ontology browsers: From 232d254396edeea99a1fa34da0cb6fd21a95c23b Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Thu, 24 Apr 2025 10:36:36 +0200 Subject: [PATCH 06/13] Update after the review bmont.md --- ontology/bmont.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index d1a21a857..c64d0b92b 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -34,5 +34,5 @@ tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue usages: - description: BMONT is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM). -activity_status: active +activity_status: true --- From f1b1f19e82e83f32daa5957f2bbe93bf3eb47f71 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Fri, 25 Apr 2025 10:43:08 +0200 Subject: [PATCH 07/13] Update ontology/bmont.md Co-authored-by: Deepak --- ontology/bmont.md | 1 - 1 file changed, 1 deletion(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index c64d0b92b..34b2339a7 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -15,7 +15,6 @@ contact: description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects. domain: health homepage: https://github.com/SCAI-BIO/BiomarkerOntology -in_foundry_order: license: label: CC BY 4.0 url: http://creativecommons.org/licenses/by/4.0/ From 8c0dd03fcf6a224d0969a10b8d0645ba616028ec Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Fri, 25 Apr 2025 10:43:52 +0200 Subject: [PATCH 08/13] Update ontology/bmont.md Co-authored-by: Deepak --- ontology/bmont.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 34b2339a7..1ab4ce58b 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -23,11 +23,6 @@ products: - id: BMONT.owl - id: bmont.obo description: Includes axioms linking to other ontologies, but no imports of those ontologies -publications: -- id: - title: -- id: - title: Using ontologies to describe mouse phenotypes repository: https://github.com/SCAI-BIO/BiomarkerOntology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue usages: From b663315469f04c07b15cad6ffd082996512a119f Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Fri, 25 Apr 2025 10:49:40 +0200 Subject: [PATCH 09/13] Update ontology/bmont.md Co-authored-by: Deepak --- ontology/bmont.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 1ab4ce58b..b725843ea 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -6,7 +6,7 @@ title: Biomarker Ontology browsers: - title: BioPortal Ontology Browser label: BioPortal - url: [https://bioportal.bioontology.org/ontologies/BMONT] + url: https://bioportal.bioontology.org/ontologies/BMONT contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil From 3302725c42d676309b3b60228a77a3e255182d3e Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Fri, 25 Apr 2025 10:55:12 +0200 Subject: [PATCH 10/13] Update ontology/bmont.md Co-authored-by: Deepak --- ontology/bmont.md | 1 - 1 file changed, 1 deletion(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index b725843ea..8e12dafe1 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -1,6 +1,5 @@ --- layout: ontology_detail -layout: ontology_detail id: bmont title: Biomarker Ontology browsers: From d72a871e7a24ec0246f689b7a9663c9995a0e830 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Sat, 3 May 2025 11:52:10 +0200 Subject: [PATCH 11/13] Update ontology/bmont.md Usage description is removed as the usage is not yet documented. Co-authored-by: Deepak --- ontology/bmont.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 8e12dafe1..39a78ae08 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -24,8 +24,6 @@ products: description: Includes axioms linking to other ontologies, but no imports of those ontologies repository: https://github.com/SCAI-BIO/BiomarkerOntology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue -usages: -- description: BMONT is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM). activity_status: true --- From 68346dc812d0d6f4959b99cf6daa8cd88d235170 Mon Sep 17 00:00:00 2001 From: Astghik-S <60783513+Astghik-S@users.noreply.github.com> Date: Sat, 3 May 2025 11:54:07 +0200 Subject: [PATCH 12/13] Update bmont.md bmont.obo is deleted as it is not existing. --- ontology/bmont.md | 1 - 1 file changed, 1 deletion(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 39a78ae08..05068f606 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -20,7 +20,6 @@ license: preferredPrefix: BMONT products: - id: BMONT.owl -- id: bmont.obo description: Includes axioms linking to other ontologies, but no imports of those ontologies repository: https://github.com/SCAI-BIO/BiomarkerOntology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue From d175e3f2cfbf15498701009b54e27fb0efa30bc7 Mon Sep 17 00:00:00 2001 From: Deepak Date: Tue, 6 May 2025 11:58:31 +0200 Subject: [PATCH 13/13] Fix 'activity_status' --- ontology/bmont.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/ontology/bmont.md b/ontology/bmont.md index 05068f606..fc1f62dc2 100644 --- a/ontology/bmont.md +++ b/ontology/bmont.md @@ -23,6 +23,5 @@ products: description: Includes axioms linking to other ontologies, but no imports of those ontologies repository: https://github.com/SCAI-BIO/BiomarkerOntology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue - -activity_status: true +activity_status: active ---