Merge pull request #1954 from FlyBase/release_2024-12-05

Release 2024-12-05

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.2
+    container: obolibrary/odkfull:v1.5.4
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for fbbt
 # Generated using ontology-development-kit
-# ODK Version: v1.5.2
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use fbbt.Makefile instead
 
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.5.2
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')

src/ontology/components/VFB_xrefs.owl

@@ -18871,14 +18871,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/FBbt_00006047 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00006047">
-        <oboInOwl:hasDbXref>VFB:FBbt_00006047</oboInOwl:hasDbXref>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/FBbt_00006048 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00006048">
@@ -37423,14 +37415,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/FBbt_00048887 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00048887">
-        <oboInOwl:hasDbXref>VFB:FBbt_00048887</oboInOwl:hasDbXref>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/FBbt_00048888 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00048888">
@@ -63839,6 +63823,14 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053250 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053250">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053250</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/FBbt_00053258 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053258">
@@ -63967,6 +63959,14 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053278 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053278">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053278</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/FBbt_00053279 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053279">
@@ -64047,6 +64047,158 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053293 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053293">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053293</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053294 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053294">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053294</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053295 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053295">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053295</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053296 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053296">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053296</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053297 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053297">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053297</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053298 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053298">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053298</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053299 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053299">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053299</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053300 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053300">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053300</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053301 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053301">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053301</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053302 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053302">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053302</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053303 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053303">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053303</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053304 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053304">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053304</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053305 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053305">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053305</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053306 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053306">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053306</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053307 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053307">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053307</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053308 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053308">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053308</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053309 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053309">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053309</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053310 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053310">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053310</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/FBbt_00053311 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00053311">
+        <oboInOwl:hasDbXref>VFB:FBbt_00053311</oboInOwl:hasDbXref>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/FBbt_00058013 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00058013">

src/ontology/fbbt-edit.obo

@@ -8676,7 +8676,7 @@ relationship: BFO:0000050 FBbt:00000155 ! part of embryonic head
 [Term]
 id: FBbt:00001059
 name: visual primordium
-def: "Primordium that develops from the posterior procephalic region of the embryo and gives rise to visual structures of the larva and adult (Green et al., 1993; Chang et al., 2001). An optic placode forms from cells of the the visual primordium when they become columnar in shape towards the end of stage 11 (Green et al., 1993; Chang et al., 2001). This placode invaginates during stages 12-13, forming a deep pouch of approximately 85 cells (Green et al., 1993). Its ventral lip segregates from the rest of the primordium and develops into the Bolwig organ (Green et al., 1993). The remainder of the placode, which will form the optic lobe, detaches from the surface of the embryo and attaches to the lateral brain, maintaining a tubular appearance until larval hatching (Green et al., 1993). Its anterior and posterior domains will become the larval inner and outer optic anlage, respectively (Chang et al., 2001). The cells that will become the eye disc are anterior and dorsal to the optic lobe placode cells (Chang et al., 2001). They move into the interior of the embryo during head involution, when they are pushed under the dorsal ridge (Huang et al., 2017)." [FlyBase:FBrf0064481, FlyBase:FBrf0141490, FlyBase:FBrf0235170, FlyBase:FBrf0243080]
+def: "Primordium that develops from the posterior procephalic region of the embryo and gives rise to visual structures of the larva and adult (Green et al., 1993; Chang et al., 2001). An optic placode forms from cells of the visual primordium when they become columnar in shape towards the end of stage 11 (Green et al., 1993; Chang et al., 2001). This placode invaginates during stages 12-13, forming a deep pouch of approximately 85 cells (Green et al., 1993). Its ventral lip segregates from the rest of the primordium and develops into the Bolwig organ (Green et al., 1993). The remainder of the placode, which will form the optic lobe, detaches from the surface of the embryo and attaches to the lateral brain, maintaining a tubular appearance until larval hatching (Green et al., 1993). Its anterior and posterior domains will become the larval inner and outer optic anlage, respectively (Chang et al., 2001). The cells that will become the eye disc are anterior and dorsal to the optic lobe placode cells (Chang et al., 2001). They move into the interior of the embryo during head involution, when they are pushed under the dorsal ridge (Huang et al., 2017)." [FlyBase:FBrf0064481, FlyBase:FBrf0141490, FlyBase:FBrf0235170, FlyBase:FBrf0243080]
 subset: cur
 subset: EmbDevSlim
 synonym: "optic lobe placode" NARROW [FlyBase:FBrf0141490]
@@ -46865,7 +46865,7 @@ relationship: RO:0002202 FBbt:00005324 ! develops from stage 10 embryo
 [Term]
 id: FBbt:00005326
 name: stomodeal invagination
-def: "Infolding of the anteroventral embryo that arises during stage 10 (Campos-Ortega and Hartenstein, 1997). Its formation begins when cells surrounding the stomodeal anlage, which consists of a plate of tall cylindrical cells just prior to invagination, divide synchronously (Campos-Ortega and Hartenstein, 1997). The invaginated cells divide immediately afterwards, forming a monolayered epithelium (Campos-Ortega and Hartenstein, 1997). It is initially oriented perpendicular to the horizontal plane, but progressively bends towards the ventral plane (Campos-Ortega and Hartenstein, 1997). It grows caudalwards by cell divisions and incorporation of neighboring ectodermal cells (Campos-Ortega and Hartenstein, 1997)." [FlyBase:FBrf0089570]
+def: "Infolding of the anteroventral embryo that arises during stage 10 (Campos-Ortega and Hartenstein, 1997). Its formation begins when cells surrounding the stomodeal anlage, which consists of a plate of tall cylindrical cells just prior to invagination, divide synchronously (Campos-Ortega and Hartenstein, 1997). The invaginated cells divide immediately afterwards, forming a monolayered epithelium (Campos-Ortega and Hartenstein, 1997). It is initially oriented perpendicular to the horizontal plane, but progressively bends towards the ventral plane (Campos-Ortega and Hartenstein, 1997). It grows caudally by cell divisions and incorporation of neighboring ectodermal cells (Campos-Ortega and Hartenstein, 1997)." [FlyBase:FBrf0089570]
 subset: cur
 synonym: "anterior midgut invagination" RELATED []
 synonym: "stomodeum" BROAD [FlyBase:FBrf0089570]
@@ -50539,7 +50539,7 @@ relationship: BFO:0000050 FBbt:00003138 ! part of adult midgut
 [Term]
 id: FBbt:00005830
 name: Bolwig organ primordium
-def: "Primordium of the embryo that gives rise to the larval Bolwig organ. It develops from the most posterior region of the visual primordium, remaining attached to the surface as the the rest of the optic placode becomes internalized during stages 12-13 (Green et al., 1993). It consists of approximately 12 cells, which begin to differentiate into photoreceptors during stage 13 (Green et al., 1993). During stages 15-16, the photoreceptors move out of the epidermis and come to lie attached to the outer lining of the dorsal pouch (Green et al., 1993)." [FlyBase:FBrf0064481, FlyBase:FBrf0089570, FlyBase:FBrf0151275, FlyBase:FBrf0243080]
+def: "Primordium of the embryo that gives rise to the larval Bolwig organ. It develops from the most posterior region of the visual primordium, remaining attached to the surface as the rest of the optic placode becomes internalized during stages 12-13 (Green et al., 1993). It consists of approximately 12 cells, which begin to differentiate into photoreceptors during stage 13 (Green et al., 1993). During stages 15-16, the photoreceptors move out of the epidermis and come to lie attached to the outer lining of the dorsal pouch (Green et al., 1993)." [FlyBase:FBrf0064481, FlyBase:FBrf0089570, FlyBase:FBrf0151275, FlyBase:FBrf0243080]
 subset: cur
 subset: EmbDevSlim
 synonym: "Bolwig's organ primordium" EXACT []
@@ -56866,7 +56866,7 @@ property_value: http://purl.org/dc/terms/date "2010-04-13T03:52:50Z" xsd:dateTim
 [Term]
 id: FBbt:00007454
 name: adult antennal lobe projection neuron VM7v adPN
-def: "Adult uniglomerular antennal lobe projection neuron from the ad neuroblast lineage with dendrites that mainly innervate antennal lobe glomerulus VM7v (also known as glomerulus 1). This is the eigth cell type to be generated post-embryonically by neuroblast ALad1 (Yu et al., 2010). There are around two of these per hemisphere, they fasciculate with the medial antennal lobe tract and they are cholinergic (Yu et al., 2010; Bates et al., 2020)." [FlyBase:FBrf0146917, FlyBase:FBrf0211729, FlyBase:FBrf0246460]
+def: "Adult uniglomerular antennal lobe projection neuron from the ad neuroblast lineage with dendrites that mainly innervate antennal lobe glomerulus VM7v (also known as glomerulus 1). This is the eighth cell type to be generated post-embryonically by neuroblast ALad1 (Yu et al., 2010). There are around two of these per hemisphere, they fasciculate with the medial antennal lobe tract and they are cholinergic (Yu et al., 2010; Bates et al., 2020)." [FlyBase:FBrf0146917, FlyBase:FBrf0211729, FlyBase:FBrf0246460]
 comment: For image, see FBrf0211729.1 adPN has been renamed to VM7v to be consistent with the change of glomerulus name from glomerulus 1 to glomerulus VM7v.
 subset: olfactory_system_draft
 synonym: "1 adPN" EXACT [FlyBase:FBrf0146917]
@@ -106008,14 +106008,14 @@ property_value: http://purl.org/dc/terms/date "2021-08-19T12:00:00Z" xsd:dateTim
 [Term]
 id: FBbt:00051473 ! hemilineage 22B secondary neuron
 def: "Any hemilineage B (Notch OFF) neuron that develops from neuroblast NB5-4 during the postembryonic phase of neurogenesis. In the adult, these neurons are glutamatergic (Lacin et al., 2019)." [FlyBase:FBrf0242251]
-comment: Presumed to be motor neurons (Lacin et al., 2019)
+comment: Presumed to be motor neurons (Lacin et al., 2019).
 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1373-1705
 property_value: http://purl.org/dc/terms/date "2021-08-19T12:00:00Z" xsd:dateTime
 
 [Term]
 id: FBbt:00051474 ! hemilineage 20B secondary neuron
 def: "Any hemilineage B (Notch OFF) neuron that develops from neuroblast NB5-7 during the postembryonic phase of neurogenesis. In the adult, these neurons are glutamatergic (Lacin et al., 2019)." [FlyBase:FBrf0242251]
-comment: Presumed to be motor neurons (Lacin et al., 2019)
+comment: Presumed to be motor neurons (Lacin et al., 2019).
 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1373-1705
 property_value: http://purl.org/dc/terms/date "2021-08-19T12:00:00Z" xsd:dateTime
 
@@ -124701,7 +124701,7 @@ property_value: http://purl.org/dc/terms/date "2024-11-18T18:21:55Z" xsd:dateTim
 [Term]
 id: FBbt:00053296
 name: larval optic anlage palisade glial cell
-def: "Larval glial cell that arises from a medulla glial cell (Plazaola-Sasieta et al., 2019). These cells form a barrier beween the developing lamina and lobula plate (Plazaola-Sasieta et al., 2019)." [FlyBase:FBrf0243725]
+def: "Larval glial cell that arises from a medulla glial cell (Plazaola-Sasieta et al., 2019). These cells form a barrier between the developing lamina and lobula plate (Plazaola-Sasieta et al., 2019)." [FlyBase:FBrf0243725]
 comment: Distinct from chiasma and satellite glia, but unknown what (if anything) these cells become in the adult (Plazaola-Sasieta et al., 2019).
 synonym: "larval pag" EXACT [FlyBase:FBrf0243725]
 is_a: FBbt:00001251 ! larval glial cell
@@ -171194,8 +171194,8 @@ relationship: RO:0002292 http://flybase.org/reports/FBgn0004110 ! expresses tin
 [Term]
 id: FBbt:10005349
 name: cephalic vascular rudiment
-def: "Structure extending dorsal to the late embryonic or larval esophagus and contacting the aorta (de Valesco et al., 2004)." [FlyBase:FBrf0179777]
-comment: This is an evolutionary vestige of the cephalic aorta found in other insect species (de Valesco et al., 2004). Only studied in embryo.
+def: "Structure extending dorsal to the late embryonic or larval esophagus and contacting the aorta (de Velasco et al., 2004)." [FlyBase:FBrf0179777]
+comment: This is an evolutionary vestige of the cephalic aorta found in other insect species (de Velasco et al., 2004). Only studied in embryo.
 subset: cur
 subset: EmbDevSlim
 synonym: "cephalic vascular remnant" EXACT [FlyBase:FBrf0219253]

src/ontology/fbbt.Makefile

@@ -224,6 +224,9 @@ $(COMPONENTSDIR)/mappings_xrefs.owl: $(MAPPINGDIR)/fbbt.sssom.tsv $(SCRIPTSDIR)/
 # Ensure the mapping set is published along with the other artefacts
 RELEASE_ASSETS_AFTER_RELEASE += ../../fbbt.sssom.tsv
 
+# Also publish the synonyms with EM source
+RELEASE_ASSETS_AFTER_RELEASE += ../../EM_synonyms.owl
+
 #####################################################################################
 ### Generate the flybase anatomy version of FBBT
 #####################################################################################