From f26501a8eca07f5009b0a82756cfbcfb564fb049 Mon Sep 17 00:00:00 2001 From: Seyed Yahya Shirazi Date: Tue, 30 Jul 2024 10:23:03 -0700 Subject: [PATCH 1/6] Add exemplar tags --- .../HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv | 3 ++- .../hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv | 13 ++++++++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv index fe9672c..e5d62ba 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv @@ -7,4 +7,5 @@ owl: http://www.w3.org/2002/07/owl# The OWL namespace [OWL2-OVERVIEW] prov: http://www.w3.org/ns/prov# The PROV namespace [PROV-DM] dc: http://purl.org/dc/elements/1.1/ The Dublin Core elements terms: http://purl.org/dc/terms/ The Dublin Core terms -foaf: http://xmlns.com/foaf/0.1/ Friend-of-a-Friend http://xmlns.com/foaf/spec/ \ No newline at end of file +foaf: http://xmlns.com/foaf/0.1/ Friend-of-a-Friend http://xmlns.com/foaf/spec/ +has_dbxref http://www.geneontology.org/formats/oboInOwl#dbxref Relates an entity to an external database entry \ No newline at end of file diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv index 952c833..3f6e615 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv @@ -1,2 +1,13 @@ hedId rdfs:label Level omn:SubClassOf Attributes dc:description omn:EquivalentTo Annotations - Anatomical-landmark 0 Anatomical-item rooted=Anatomical-item A collection of specific points on the human body used for anatomical and sensor placement reference. dc:source "Original", rdfs:comment "Body landmarks are used to standardize sensor placement." + Anatomical-landmark 0 Anatomical-item rooted=Anatomical-item A collection of specific points on the human body used for anatomical and sensor placement reference. dc:source "Original", rdfs:comment "Body landmarks are used to standardize sensor placement. + Head-landmark 1 Anatomical-landmarks Points on the head used as reference landmarks. dc:source "Original" + Nasion 2 Head-landmark The midpoint between the eyes just above the bridge of the nose. + Inion 2 Head-landmark The most prominent point of the occipital bone at the back of the head. + Left Helix-Tragus Junction (LHJ) 2 Head-landmark The point where the helix meets the tragus of the left ear. + Right Helix-Tragus Junction (RHJ) 2 Head-landmark The point where the helix meets the tragus of the right ear. + Vertex 2 Head-landmark The highest point on the head in the midline. + Mastoid-process 2 Head-landmark dc:source "Original" + Torso-chest-landmark 1 Anatomical-landmarks Points on the chest used as reference landmarks. dc:source "Original" + Acromion-process 2 Torso-chest-landmark The outermost point of the shoulder blade. has_dbxref: "NCIT:C32048" "FMA:12525" "UBERON:0002497" + Vertebra-prominens (C7) 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. has_dbxref: "NCIT:C32245" "FMA:23260" "UBERON:0004616" + Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. has_dbxref: "NCIT:C33895" "FMA:7488" "UBERON:0002207" \ No newline at end of file From a7d0236fb7129d3d4029aba315221abaf80422e8 Mon Sep 17 00:00:00 2001 From: Seyed Yahya Shirazi Date: Wed, 31 Jul 2024 14:27:49 -0700 Subject: [PATCH 2/6] Correct syntax --- .../hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv | 3 ++- .../prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv | 6 +++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv index e5d62ba..16e0090 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv @@ -8,4 +8,5 @@ prov: http://www.w3.org/ns/prov# The PROV namespace [PROV-DM] dc: http://purl.org/dc/elements/1.1/ The Dublin Core elements terms: http://purl.org/dc/terms/ The Dublin Core terms foaf: http://xmlns.com/foaf/0.1/ Friend-of-a-Friend http://xmlns.com/foaf/spec/ -has_dbxref http://www.geneontology.org/formats/oboInOwl#dbxref Relates an entity to an external database entry \ No newline at end of file +obo: http://purl.obolibrary.org/obo/ Open Biomedical Ontologies +has_dbxref: http://www.geneontology.org/formats/oboInOwl#dbxref Relates an entity to an external database entry \ No newline at end of file diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv index 3f6e615..4502aa4 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv @@ -8,6 +8,6 @@ hedId rdfs:label Level omn:SubClassOf Attributes dc:description omn:EquivalentTo Vertex 2 Head-landmark The highest point on the head in the midline. Mastoid-process 2 Head-landmark dc:source "Original" Torso-chest-landmark 1 Anatomical-landmarks Points on the chest used as reference landmarks. dc:source "Original" - Acromion-process 2 Torso-chest-landmark The outermost point of the shoulder blade. has_dbxref: "NCIT:C32048" "FMA:12525" "UBERON:0002497" - Vertebra-prominens (C7) 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. has_dbxref: "NCIT:C32245" "FMA:23260" "UBERON:0004616" - Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. has_dbxref: "NCIT:C33895" "FMA:7488" "UBERON:0002207" \ No newline at end of file + Acromion-process 2 Torso-chest-landmark The outermost point of the shoulder blade. obo:has_dbxref "NCIT:C32048", obo:has_dbxref "FMA:12525", obo:has_dbxref "UBERON:0002497" + Vertebra-prominens (C7) 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. obo:has_dbxref "NCIT:C32245", obo:has_dbxref "FMA:23260", obo:has_dbxref "UBERON:0004616" + Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. obo:has_dbxref "NCIT:C33895", obo:has_dbxref "FMA:7488", obo:has_dbxref "UBERON:0002207" \ No newline at end of file From 09ce3ba205bce6d5635e7f79e55943ff3e119d19 Mon Sep 17 00:00:00 2001 From: Seyed Yahya Shirazi Date: Thu, 1 Aug 2024 09:01:01 -0700 Subject: [PATCH 3/6] Move `has_dbxrf` to AnnotPropExtr. --- .../HED_slam_1.0.0_AnnotationPropertyExternal.tsv | 3 ++- .../hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv | 1 - 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_AnnotationPropertyExternal.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_AnnotationPropertyExternal.tsv index 982468f..de03598 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_AnnotationPropertyExternal.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_AnnotationPropertyExternal.tsv @@ -13,4 +13,5 @@ dc: subject dc: title dc: type foaf: homepage -terms: license \ No newline at end of file +terms: license +obo: has_dbxref \ No newline at end of file diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv index 16e0090..c77bc76 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Prefixes.tsv @@ -9,4 +9,3 @@ dc: http://purl.org/dc/elements/1.1/ The Dublin Core elements terms: http://purl.org/dc/terms/ The Dublin Core terms foaf: http://xmlns.com/foaf/0.1/ Friend-of-a-Friend http://xmlns.com/foaf/spec/ obo: http://purl.obolibrary.org/obo/ Open Biomedical Ontologies -has_dbxref: http://www.geneontology.org/formats/oboInOwl#dbxref Relates an entity to an external database entry \ No newline at end of file From da2cf99e2e00fb320d1da54f8fa31b9721c55531 Mon Sep 17 00:00:00 2001 From: Seyed Yahya Shirazi Date: Thu, 1 Aug 2024 09:48:41 -0700 Subject: [PATCH 4/6] Correct table syntax --- .../hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv index 4502aa4..44f6f1f 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv @@ -1,13 +1,13 @@ hedId rdfs:label Level omn:SubClassOf Attributes dc:description omn:EquivalentTo Annotations Anatomical-landmark 0 Anatomical-item rooted=Anatomical-item A collection of specific points on the human body used for anatomical and sensor placement reference. dc:source "Original", rdfs:comment "Body landmarks are used to standardize sensor placement. - Head-landmark 1 Anatomical-landmarks Points on the head used as reference landmarks. dc:source "Original" + Head-landmark 1 Anatomical-landmark Points on the head used as reference landmarks. dc:source "Original" Nasion 2 Head-landmark The midpoint between the eyes just above the bridge of the nose. Inion 2 Head-landmark The most prominent point of the occipital bone at the back of the head. - Left Helix-Tragus Junction (LHJ) 2 Head-landmark The point where the helix meets the tragus of the left ear. - Right Helix-Tragus Junction (RHJ) 2 Head-landmark The point where the helix meets the tragus of the right ear. + Left-helix-tragus-junction-LHJ 2 Head-landmark The point where the helix meets the tragus of the left ear. + Right-helix-tragus-junction-RHJ 2 Head-landmark The point where the helix meets the tragus of the right ear. Vertex 2 Head-landmark The highest point on the head in the midline. Mastoid-process 2 Head-landmark dc:source "Original" Torso-chest-landmark 1 Anatomical-landmarks Points on the chest used as reference landmarks. dc:source "Original" Acromion-process 2 Torso-chest-landmark The outermost point of the shoulder blade. obo:has_dbxref "NCIT:C32048", obo:has_dbxref "FMA:12525", obo:has_dbxref "UBERON:0002497" - Vertebra-prominens (C7) 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. obo:has_dbxref "NCIT:C32245", obo:has_dbxref "FMA:23260", obo:has_dbxref "UBERON:0004616" + Vertebra-prominens-C7 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. obo:has_dbxref "NCIT:C32245", obo:has_dbxref "FMA:23260", obo:has_dbxref "UBERON:0004616" Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. obo:has_dbxref "NCIT:C33895", obo:has_dbxref "FMA:7488", obo:has_dbxref "UBERON:0002207" \ No newline at end of file From e1431b0bc4fbc94b227d720ca1b334fdfe2b08f2 Mon Sep 17 00:00:00 2001 From: Seyed Yahya Shirazi Date: Thu, 1 Aug 2024 09:50:33 -0700 Subject: [PATCH 5/6] Another correction --- .../prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv index 44f6f1f..ad0fe43 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv @@ -7,7 +7,7 @@ hedId rdfs:label Level omn:SubClassOf Attributes dc:description omn:EquivalentTo Right-helix-tragus-junction-RHJ 2 Head-landmark The point where the helix meets the tragus of the right ear. Vertex 2 Head-landmark The highest point on the head in the midline. Mastoid-process 2 Head-landmark dc:source "Original" - Torso-chest-landmark 1 Anatomical-landmarks Points on the chest used as reference landmarks. dc:source "Original" + Torso-chest-landmark 1 Anatomical-landmark Points on the chest used as reference landmarks. dc:source "Original" Acromion-process 2 Torso-chest-landmark The outermost point of the shoulder blade. obo:has_dbxref "NCIT:C32048", obo:has_dbxref "FMA:12525", obo:has_dbxref "UBERON:0002497" Vertebra-prominens-C7 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. obo:has_dbxref "NCIT:C32245", obo:has_dbxref "FMA:23260", obo:has_dbxref "UBERON:0004616" Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. obo:has_dbxref "NCIT:C33895", obo:has_dbxref "FMA:7488", obo:has_dbxref "UBERON:0002207" \ No newline at end of file From c67d1651686318ef2110398910ca866ceec315bc Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Thu, 1 Aug 2024 16:51:15 +0000 Subject: [PATCH 6/6] Automated schema changes --- .../slam/prerelease/HED_slam_1.0.0.mediawiki | 11 +++ .../slam/prerelease/HED_slam_1.0.0.xml | 87 +++++++++++++++++++ .../HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv | 6 +- 3 files changed, 101 insertions(+), 3 deletions(-) diff --git a/library_schemas/slam/prerelease/HED_slam_1.0.0.mediawiki b/library_schemas/slam/prerelease/HED_slam_1.0.0.mediawiki index 613580c..6aae5c5 100644 --- a/library_schemas/slam/prerelease/HED_slam_1.0.0.mediawiki +++ b/library_schemas/slam/prerelease/HED_slam_1.0.0.mediawiki @@ -6,6 +6,17 @@ The HED SLAM(Sensor Location and Motion) HED library schema is designed to stand !# start schema '''Anatomical-landmark''' {rooted=Anatomical-item} [A collection of specific points on the human body used for anatomical and sensor placement reference.] +* Head-landmark [Points on the head used as reference landmarks.] +** Inion [The most prominent point of the occipital bone at the back of the head.] +** Left-helix-tragus-junction-LHJ [The point where the helix meets the tragus of the left ear.] +** Mastoid-process +** Nasion [The midpoint between the eyes just above the bridge of the nose.] +** Right-helix-tragus-junction-RHJ [The point where the helix meets the tragus of the right ear.] +** Vertex [The highest point on the head in the midline.] +* Torso-chest-landmark [Points on the chest used as reference landmarks.] +** Acromion-process [The outermost point of the shoulder blade.] +** Vertebra-prominens-C7 [The seventh cervical vertebra at the base of the neck.] +** Xiphoid-process [The small cartilaginous process at the lower end of the sternum.] !# end schema diff --git a/library_schemas/slam/prerelease/HED_slam_1.0.0.xml b/library_schemas/slam/prerelease/HED_slam_1.0.0.xml index cfdcf46..06ffb5e 100644 --- a/library_schemas/slam/prerelease/HED_slam_1.0.0.xml +++ b/library_schemas/slam/prerelease/HED_slam_1.0.0.xml @@ -1512,6 +1512,93 @@ inLibrary slam + + Head-landmark + Points on the head used as reference landmarks. + + inLibrary + slam + + + Inion + The most prominent point of the occipital bone at the back of the head. + + inLibrary + slam + + + + Left-helix-tragus-junction-LHJ + The point where the helix meets the tragus of the left ear. + + inLibrary + slam + + + + Mastoid-process + + inLibrary + slam + + + + Nasion + The midpoint between the eyes just above the bridge of the nose. + + inLibrary + slam + + + + Right-helix-tragus-junction-RHJ + The point where the helix meets the tragus of the right ear. + + inLibrary + slam + + + + Vertex + The highest point on the head in the midline. + + inLibrary + slam + + + + + Torso-chest-landmark + Points on the chest used as reference landmarks. + + inLibrary + slam + + + Acromion-process + The outermost point of the shoulder blade. + + inLibrary + slam + + + + Vertebra-prominens-C7 + The seventh cervical vertebra at the base of the neck. + + inLibrary + slam + + + + Xiphoid-process + The small cartilaginous process at the lower end of the sternum. + + inLibrary + slam + + + Body diff --git a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv index ad0fe43..f029f4e 100644 --- a/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv +++ b/library_schemas/slam/prerelease/hedtsv/HED_slam_1.0.0/HED_slam_1.0.0_Tag.tsv @@ -1,13 +1,13 @@ hedId rdfs:label Level omn:SubClassOf Attributes dc:description omn:EquivalentTo Annotations Anatomical-landmark 0 Anatomical-item rooted=Anatomical-item A collection of specific points on the human body used for anatomical and sensor placement reference. dc:source "Original", rdfs:comment "Body landmarks are used to standardize sensor placement. Head-landmark 1 Anatomical-landmark Points on the head used as reference landmarks. dc:source "Original" - Nasion 2 Head-landmark The midpoint between the eyes just above the bridge of the nose. Inion 2 Head-landmark The most prominent point of the occipital bone at the back of the head. Left-helix-tragus-junction-LHJ 2 Head-landmark The point where the helix meets the tragus of the left ear. + Mastoid-process 2 Head-landmark dc:source "Original" + Nasion 2 Head-landmark The midpoint between the eyes just above the bridge of the nose. Right-helix-tragus-junction-RHJ 2 Head-landmark The point where the helix meets the tragus of the right ear. Vertex 2 Head-landmark The highest point on the head in the midline. - Mastoid-process 2 Head-landmark dc:source "Original" Torso-chest-landmark 1 Anatomical-landmark Points on the chest used as reference landmarks. dc:source "Original" Acromion-process 2 Torso-chest-landmark The outermost point of the shoulder blade. obo:has_dbxref "NCIT:C32048", obo:has_dbxref "FMA:12525", obo:has_dbxref "UBERON:0002497" Vertebra-prominens-C7 2 Torso-chest-landmark The seventh cervical vertebra at the base of the neck. obo:has_dbxref "NCIT:C32245", obo:has_dbxref "FMA:23260", obo:has_dbxref "UBERON:0004616" - Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. obo:has_dbxref "NCIT:C33895", obo:has_dbxref "FMA:7488", obo:has_dbxref "UBERON:0002207" \ No newline at end of file + Xiphoid-process 2 Torso-chest-landmark The small cartilaginous process at the lower end of the sternum. obo:has_dbxref "NCIT:C33895", obo:has_dbxref "FMA:7488", obo:has_dbxref "UBERON:0002207"