From 55e73aead89468b1b647f17cf8bc62297cfbde68 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Wed, 6 Dec 2023 08:55:39 +0000 Subject: [PATCH 1/3] SMPs --- src/ontology/fbbt-edit.obo | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/src/ontology/fbbt-edit.obo b/src/ontology/fbbt-edit.obo index 63da31f1c..148a2669d 100644 --- a/src/ontology/fbbt-edit.obo +++ b/src/ontology/fbbt-edit.obo @@ -101671,7 +101671,7 @@ property_value: IAO:0006011 FBbt:00100551 {xref="doi:10.1101/2020.06.12.148775"} [Term] id: FBbt:00049463 name: neuroblast SMPad1 -def: "Neuroblast of the brain that generates a sexually-dimorphic lineage with prominent proximal neurite elaboration in the superior medial protocerebrum (Yu et al., 2013)." [FlyBase:FBrf0221412] +def: "Neuroblast of the brain that generates a sexually-dimorphic lineage with prominent proximal neurite elaboration in the superior medial protocerebrum (Yu et al., 2013)." [FlyBase:FBrf0221412, FlyBase:FBrf0221438] xref: VFB:FBbt_00049463 is_a: FBbt:00001334 ! protocerebral neuroblast is_a: FBbt:00100532 ! type I neuroblast @@ -112023,7 +112023,7 @@ xref: VFB:FBbt_00050171 [Term] id: FBbt:00050172 name: neuroblast SMPad3 -def: "." [FlyBase:FBrf0221412] +def: "Neuroblast that produces secondary neurons with their cell bodies in the superior medial protocerebrum and arborization in the superior medial brain (Yu et al., 2013)." [FlyBase:FBrf0221412] subset: TL_lineage_clone xref: VFB:FBbt_00050172 is_a: FBbt:00001334 ! protocerebral neuroblast @@ -112295,7 +112295,7 @@ xref: VFB:FBbt_00050192 [Term] id: FBbt:00050193 name: neuroblast SMPp&v1 -def: "." [FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that produces two posterior clusters of secondary neurons, one in the dorsal brain and another more ventral (Ito et al., 2013). The clone is similar to that of SMPp&v2, but contains more neurons (Ito et al., 2013)." [FlyBase:FBrf0221412, FlyBase:FBrf0221438] subset: TL_lineage_clone synonym: "neuroblast SMPp_v1" EXACT [] xref: VFB:FBbt_00050193 @@ -112406,7 +112406,7 @@ xref: VFB:FBbt_00050200 [Term] id: FBbt:00050201 name: neuroblast SMPad2 -def: "." [FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that produces a single cluster of secondary neurons with their cell bodies in the superior medial protocerebrum (Ito et al., 2013). These descendant neurons collectively innervate many parts of the superior medial brain in one hemisphere (Ito et al., 2013)." [FlyBase:FBrf0221412, FlyBase:FBrf0221438] comment: SMPad2 mapped to DAMd2/3 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775. subset: TL_lineage_clone xref: VFB:FBbt_00050201 @@ -113006,7 +113006,7 @@ xref: VFB:FBbt_00050242 [Term] id: FBbt:00050243 name: neuroblast SMPad1 (male) -def: "." [FlyBase:FBrf0221412] +def: "." [FlyBase:FBrf0221412, FlyBase:FBrf0221438] subset: TL_lineage_clone synonym: "neuroblast SMPad1m" EXACT [] xref: VFB:FBbt_00050243 @@ -158604,7 +158604,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T11:49:54Z" xsd:dateTim [Term] id: FBbt:00100577 name: neuroblast DPMpl1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412] +def: "Neuroblast that produces a primary lineage that enters the neuropil medial to the mushroom body calyx and joins the posterior longitudinal superior medial fascicle (Hartenstein et al., 2015). Its secondary lineage has somas in the posterior ventral superior medial protocerebrum (Yu et al., 2013). In the adult, this lineage has arbors in the superior medial protocerebrum and ventral projections along the midline to the periesophageal neuropils (Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SMPpv1" EXACT [doi:10.1101/2020.06.12.148775] xref: VFB:FBbt_00100577 @@ -158802,7 +158802,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:27:40Z" xsd:dateTim [Term] id: FBbt:00100595 name: neuroblast DPLc1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that produces a primary lineage that enters the posteromedial superior lateral protocerebrum and joins the medial posterior superior transverse fascicle (Hartenstein et al., 2015). In the adult, its secondary lineage has somas clustered in the dorsal posterior superior medial protocerebrum and arbors mainly in the superior protocerebrum (Wong et al., 2013; Ito et al., 2013; Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SMPpd1" EXACT [doi:10.1101/2020.06.12.148775] xref: VFB:FBbt_00100595 @@ -158954,7 +158954,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T03:16:19Z" xsd:dateTim [Term] id: FBbt:00100608 name: neuroblast CP1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412] +def: "Neuroblast that produces a primary lineage that enters the neuropil lateral to the mushroom body calyx with projections along the median bundle (Hartenstein et al. 2015). Its secondary lineage has somas in the posterior ventral superior medial protocerebrum, arbors in the superior medial protocerebrum and inferior protocerebrum, and ventral projections along the midline to the periesophageal neuropils (Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SMPpv2" EXACT [doi:10.1101/2020.06.12.148775] xref: VFB:FBbt_00100608 @@ -166193,6 +166193,7 @@ property_value: http://purl.org/dc/terms/date "2013-05-22T11:24:12Z" xsd:dateTim id: FBbt:00110368 name: neuroblast SLPpm4 def: "." [FlyBase:FBrf0221438] +comment: Ito et al. (2013) only found two-cell clones of this lineage and note the possibility that these are first born neurons of another lineage (most likely DM1), so the 'SLPpm4' neuroblast may not exist. xref: VFB:FBbt_00110368 is_a: FBbt:00001334 ! protocerebral neuroblast is_a: FBbt:00100532 ! type I neuroblast @@ -166226,7 +166227,8 @@ property_value: http://purl.org/dc/terms/date "2013-05-22T11:24:12Z" xsd:dateTim [Term] id: FBbt:00110371 name: neuroblast SMPp&v2 -def: "." [FlyBase:FBrf0221438] +def: "Neuroblast that produces two posterior clusters of secondary neurons, one in the dorsal brain and another more ventral (Ito et al., 2013). The clone is similar to that of SMPp&v1, but contains fewer neurons (Ito et al., 2013)." [FlyBase:FBrf0221438] +comment: Only seen in one sample by Ito et al. (2013). xref: VFB:FBbt_00110371 is_a: FBbt:00001334 ! protocerebral neuroblast is_a: FBbt:00100532 ! type I neuroblast @@ -166272,7 +166274,7 @@ property_value: http://purl.org/dc/terms/date "2013-05-22T11:24:12Z" xsd:dateTim [Term] id: FBbt:00110374 name: neuroblast SMPpd2 -def: "." [FlyBase:FBrf0221438] +def: "Neuroblast that produces a secondary lineage with somas in the dorsal posterior superior medial protocerebrum and arbors in the dorsalmost part of the brain (Ito et al., 2013)." [FlyBase:FBrf0221438] xref: VFB:FBbt_00110374 is_a: FBbt:00001334 ! protocerebral neuroblast is_a: FBbt:00100532 ! type I neuroblast @@ -166701,7 +166703,8 @@ property_value: http://purl.org/dc/terms/date "2013-05-22T04:46:04Z" xsd:dateTim [Term] id: FBbt:00110411 name: neuroblast SMPad4 -def: "." [FlyBase:FBrf0221438] +def: "Neuroblast that produces secondary neurons with their somas and arborization in the superior protocerebrum (Ito et al., 2013)." [FlyBase:FBrf0221438] +comment: Ito et al. (2013) only found two-cell clones of this lineage and note the possibility that these are first born neurons of another lineage (most likely SMPad2), so the 'SMPad4' neuroblast may not exist. xref: VFB:FBbt_00110411 is_a: FBbt:00001334 ! protocerebral neuroblast is_a: FBbt:00100532 ! type I neuroblast @@ -167287,6 +167290,7 @@ property_value: http://purl.org/dc/terms/date "2013-05-23T03:45:07Z" xsd:dateTim id: FBbt:00110453 name: adult fruitless aSP-c neuron def: "Adult fruitless neuron that develops from neuroblast SMPad4 (Ito et al., 2013). There are approximately 3 of these cells per hemisphere (Cachero et al., 2010)." [FlyBase:FBrf0211926, FlyBase:FBrf0221438] +comment: Slight discrepancy here, in that SMPad4 clones only found to contain 2 neurons in Ito et al. (2013), but possible that these were only partial clones. synonym: "aSP-c neuron" EXACT [FlyBase:FBrf0211926] xref: VFB:FBbt_00110453 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5948-3092 From 90e54e1d7d734969be3bcc91e0b1613ecf01c78e Mon Sep 17 00:00:00 2001 From: Clare72 Date: Thu, 7 Dec 2023 08:28:27 +0000 Subject: [PATCH 2/3] DPLs --- src/ontology/fbbt-edit.obo | 45 +++++++++++++++++++------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/src/ontology/fbbt-edit.obo b/src/ontology/fbbt-edit.obo index 148a2669d..4e84d647f 100644 --- a/src/ontology/fbbt-edit.obo +++ b/src/ontology/fbbt-edit.obo @@ -96870,7 +96870,7 @@ property_value: http://purl.org/dc/terms/date "2020-03-19T16:17:59Z" xsd:dateTim [Term] id: FBbt:00049161 name: neuroblast DPLpv -def: "Posteriormost DPL neuroblast (Pereanu and Hartenstein, 2006; Wong et al., 2013). Cell bodies of its descendants move from a postero-dorsal position in the larva to a postero-ventral position in the adult (Lovick et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0223329, FlyBase:FBrf0229672] +def: "Posteriormost DPL neuroblast (Pereanu and Hartenstein, 2006; Wong et al., 2013). Cell bodies of its descendants move from a postero-dorsal position in the larva to a postero-ventral position in the adult (Lovick et al., 2013). Its secondary lineage arborizes in the adult ventrolateral protocerebrum and posterior lateral protocerebrum (Wong et al., 2013; Ito et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0223329, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map dorsal and ventral hemilineages of VLPp&l1 to dorsal and ventral hemilineages of DPLpv. subset: TL_lineage_clone synonym: "neuroblast VLPp&l1" EXACT [FlyBase:FBrf0246460] @@ -158741,7 +158741,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:15:52Z" xsd:dateTim [Term] id: FBbt:00100590 name: neuroblast DPLam -def: "." [FlyBase:FBrf0194268] +def: "Neuroblast that produces a primary lineage with a short tract that enters the superior lateral protocerebrum (SLP) medial to the transverse superior anterior fascicle and forms terminal arborizations in the SLP and the lateral inferior protocerebrum (Hartenstein et al., 2015). Its secondary lineage arborizes ipsilaterally in the adult superior lateral, inferior, and ventrolateral protocerebrum (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: VLPd2 listed as equivalent to DPLam in Hartenstein et al. (2017) - FBrf0234128, but DPLam mapped to VLPd1 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775, with no mapping for VLPd2. xref: VFB:FBbt_00100590 is_a: FBbt:00100745 ! neuroblast DPL @@ -158752,7 +158752,7 @@ property_value: IAO:0006011 FBbt:00050231 {xref="doi:10.1101/2020.06.12.148775"} [Term] id: FBbt:00100591 name: neuroblast DPLal1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that generates a primary lineage that enters the superior lateral protocerebrum laterally and projects a thick bundle, the transverse superior anterior fascicle, ventromedially towards the mushroom body pedunculus (Hartenstein et al., 2015). Its secondary lineage has dorsolateral somas and arborizes in the adult superior lateral protocerebrum (Wong et al., 2013; Ito et al., 2013; Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SLPal1" EXACT [FlyBase:FBrf0246460] xref: VFB:FBbt_00100591 @@ -158764,7 +158764,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:24:20Z" xsd:dateTim [Term] id: FBbt:00100592 name: neuroblast DPLal2 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that generates a primary lineage that enters the superior lateral protocerebrum laterally and projects a thick bundle, the transverse superior anterior fascicle, ventromedially towards the mushroom body pedunculus (Hartenstein et al., 2015). Its secondary lineage has arborization across the ipsilateral superior protocerebrum, including the lateral horn, and projections via the superior arch commissure to the contralateral hemisphere (Ito et al., 2013; Yu et al., 2013)" [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map lateral and medial hemilineages of LHl2 to lateral and medial hemilineages of DPLal2. subset: TL_lineage_clone synonym: "neuroblast LHl2" EXACT [FlyBase:FBrf0246460] @@ -158777,7 +158777,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:25:28Z" xsd:dateTim [Term] id: FBbt:00100593 name: neuroblast DPLal3 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that generates a primary lineage that enters the superior lateral protocerebrum laterally and projects a thick bundle, the transverse superior anterior fascicle, ventromedially towards the mushroom body pedunculus (Hartenstein et al., 2015). Its secondary lineage has somas in the anterior superior lateral protocerebrum and arbors mainly in the lateral horn and superior lateral protocerebrum (Ito et al., 2013; Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map dorsal and ventral hemilineages of SLPal2 to dorsal and ventral hemilineages of DPLal3. subset: TL_lineage_clone synonym: "neuroblast SLPal2" EXACT [FlyBase:FBrf0246460] @@ -158790,7 +158790,8 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:26:34Z" xsd:dateTim [Term] id: FBbt:00100594 name: neuroblast DPLd -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that produces a secondary lineage that enters the neuropil lateral to the tip of the mushroom body vertical lobe (Lovick et al., 2013; Hartenstein et al., 2015). In the adult, one hemilineage projects medially curving around the surface of the vertical lobe and crossing the midline in the anterior dorsal commissure, and the other projects posterolaterally, forming an anterior component of the superior lateral longitudinal fascicle (Lovick et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223329, FlyBase:FBrf0229672] +comment: Primary lineage difficult to identify in L1 (Hartenstein et al., 2015). subset: TL_lineage_clone synonym: "neuroblast LHd1" EXACT [FlyBase:FBrf0246460] xref: VFB:FBbt_00100594 @@ -158814,7 +158815,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:29:07Z" xsd:dateTim [Term] id: FBbt:00100596 name: neuroblast DPLc2 -def: "." [FlyBase:FBrf0194268] +def: "Neuroblast that produces a primary lineage that enters the posteromedial superior lateral protocerebrum (Hartenstein et al., 2015). It forms a paired lineage with DPLc4 that contributes to the posterior superior transverse fascicle and arborizes in the ipsilateral adult protocerebrum (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: CLp1 mapped to DPLc2/4 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775. xref: VFB:FBbt_00100596 is_a: FBbt:00100745 ! neuroblast DPL @@ -158825,7 +158826,7 @@ property_value: IAO:0006011 FBbt:00050204 {xref="doi:10.1101/2020.06.12.148775"} [Term] id: FBbt:00100597 name: neuroblast DPLc3 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412] +def: "Neuroblast that produces a primary lineage that enters the posteromedial superior lateral protocerebrum and joins the medial posterior superior transverse fascicle (Hartenstein et al., 2015). Its secondary lineage has somas in the dorsomedial brain and projects laterally to arborize in the superior intermediate protocerebrum (Wong et al., 2013; Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0223298, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SLPpm3" EXACT [FlyBase:FBrf0246460] xref: VFB:FBbt_00100597 @@ -158837,7 +158838,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:31:24Z" xsd:dateTim [Term] id: FBbt:00100598 name: neuroblast DPLc4 -def: "." [FlyBase:FBrf0194268] +def: "Neuroblast that produces a primary lineage that enters the posteromedial superior lateral protocerebrum (Hartenstein et al., 2015). It forms a paired lineage with DPLc2 that contributes to the posterior superior transverse fascicle and arborizes in the ipsilateral adult protocerebrum (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: CLp1 mapped to DPLc2/4 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775. xref: VFB:FBbt_00100598 is_a: FBbt:00100745 ! neuroblast DPL @@ -158848,8 +158849,7 @@ property_value: IAO:0006011 FBbt:00050204 {xref="doi:10.1101/2020.06.12.148775"} [Term] id: FBbt:00100599 name: neuroblast DPLc5 -def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +def: "Neuroblast that produces a primary lineage that enters the posteromedial superior lateral protocerebrum (SLP) and joins the medial posterior superior transverse fascicle (Hartenstein et al., 2015). It produces two secondary hemilineages that move apart from one another during development (Wong et al., 2013). The anterior hemilineage enters the neuropil alongside the DPLc1-4 lineages, extending anteromedially into the anterior superior medial protocerebrum (SMP) and part of the SLP and forming arborizations that also spread into the inferior protocerebrum (IP) (Wong et al., 2013). The posterior hemilineage has somas in the ventroposterior brain and projects anterodorsally, joining the longitudinal superior medial fascicle and crossing the midline in the anterior–dorsal commissure, its arbors overlap with those of the anterior hemilineage in the SMP and IP (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] xref: VFB:FBbt_00100599 is_a: FBbt:00100745 ! neuroblast DPL property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158858,7 +158858,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:33:36Z" xsd:dateTim [Term] id: FBbt:00100600 name: neuroblast DPLl1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that forms a primary lineage that enters the superior lateral protocerebrum lateroposteriorly and projects anteriorly, forming the longitudinal superior lateral fascicle (Hartenstein et al., 2015). In the adult, its secondary lineage has somas in the anterior superior lateral protocerebrum and arborization mainly in the superior porotcerebrum and posterior lateral protocerebrum (Ito et al., 2013; Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SLPpl1" EXACT [FlyBase:FBrf0246460] xref: VFB:FBbt_00100600 @@ -158870,7 +158870,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:35:11Z" xsd:dateTim [Term] id: FBbt:00100601 name: neuroblast DPLl2 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that forms a primary lineage that enters the superior lateral protocerebrum lateroposteriorly and projects anteriorly, forming the longitudinal superior lateral fascicle (Hartenstein et al., 2015). At the larval stage the DPLl2 and DPLl3 lineages are indistinguishable (Wong et al., 2013). In the adult, an anterior hemilineage forms a ventral projection to the dorsal ventrolateral protocerebrum and a posterior hemilineage arborizes in multiple regions of the protocerebrum (Wong et al., 2013). Projections are relatively dense compared to the DPLl3 lineage (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map anterior and posterior hemilineages of VLPd&p1 to anterior and posterior hemilineages of DPLl2. subset: TL_lineage_clone synonym: "neuroblast VLPd&p1" EXACT [FlyBase:FBrf0246460] @@ -158884,7 +158884,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:36:29Z" xsd:dateTim [Term] id: FBbt:00100602 name: neuroblast DPLl3 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that forms a primary lineage that enters the superior lateral protocerebrum lateroposteriorly and projects anteriorly, forming the longitudinal superior lateral fascicle (Hartenstein et al., 2015). At the larval stage the DPLl2 and DPLl3 lineages are indistinguishable (Wong et al., 2013). In the adult, an anterior hemilineage forms a ventral projection to the dorsal ventrolateral protocerebrum and a posterior hemilineage arborizes in multiple regions of the protocerebrum (Wong et al., 2013). Projections are relatively diffuse compared to the DPLl2 lineage (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) map anterior and posterior hemilineages of SLPad1 to anterior and posterior hemilineages of DPLl3. subset: TL_lineage_clone synonym: "neuroblast SLPad1" EXACT [doi:10.1101/2020.06.12.148775] @@ -158897,7 +158897,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:37:48Z" xsd:dateTim [Term] id: FBbt:00100603 name: neuroblast DPLp1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that forms a primary lineage with somas lateral to the larval mushroom body calyx, along with DPLp2, its tract converges onto the dorsal CP2/3 tract and enters the oblique posterior (obP) fascicle (Hartenstein et al., 2015) In the adult, its secondary lineage is also similar to that of DPLp2, entering the posterolateral neuropil surface at the base of the lateral horn and arborizing in the lateral horn and superior lateral protocerebrum (Wong et al., 2013). A long, medial branch follows the obP fascicle, crossing the mushroom body pedunculus and the brain midline, forming terminal arborizations along its trajectory in the posterior inferior protocerebrum of both hemispheres (Wong et al., 2013). A massive projection is directed ventrally along the vertical posterior tract into the posterior lateral protocerebrum and posterior wedge (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map lateral and medial hemilineages of LHp2 to lateral and medial hemilineages of DPLp1. subset: TL_lineage_clone synonym: "neuroblast LHp2" EXACT [FlyBase:FBrf0246460] @@ -158910,7 +158910,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:38:50Z" xsd:dateTim [Term] id: FBbt:00100604 name: neuroblast DPLp2 -def: "." [FlyBase:FBrf0194268] +def: "Neuroblast that forms a primary lineage with somas lateral to the larval mushroom body calyx, along with DPLp1, its tract converges onto the dorsal CP2/3 tract and enters the oblique posterior tract (Hartenstein et al., 2015). In the adult, its secondary lineage is also similar to that of DPLp1, entering the posterolateral neuropil surface at the base of the lateral horn and arborizing in the lateral horn and superior lateral protocerebrum (Wong et al., 2013). A long, medial branch follows the obP fascicle, crossing the mushroom body pedunculus and the brain midline, forming terminal arborizations along its trajectory in the posterior inferior protocerebrum of both hemispheres (Wong et al., 2013). A massive projection is directed ventrally along the vertical posterior tract into the posterior lateral protocerebrum and posterior wedge (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map the posterior hemilineage of SLPp&v1 to the posterior hemilineage of DPLp2. xref: VFB:FBbt_00100604 is_a: FBbt:00100745 ! neuroblast DPL @@ -158921,7 +158921,7 @@ property_value: IAO:0006011 FBbt:00050234 {xref="doi:10.1101/2020.06.12.148775"} [Term] id: FBbt:00100605 name: neuroblast DPLm1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that forms a primary lineage paired with that of DPLm2, having somas lateral to the larval mushroom body calyx and a short tract that enters the posterior superior lateral protocerebrum and projects anteriorly (Hartenstein et al., 2015). Its secondary lineage mainly arborizes in the adult superior lateral and intermediate protocerebrum (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SLPpm1" EXACT [doi:10.1101/2020.06.12.148775] xref: VFB:FBbt_00100605 @@ -158933,8 +158933,8 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T02:41:19Z" xsd:dateTim [Term] id: FBbt:00100606 name: neuroblast DPLm2 -def: "." [FlyBase:FBrf0194268] -comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map the dorsal hemilineage of LHd2 to the dorsal hemilineage of DPLm2. +def: "Neuroblast that forms a primary lineage paired with that of DPLm1, having somas lateral to the larval mushroom body calyx and a short tract that enters the posterior superior lateral protocerebrum and projects anteriorly (Hartenstein et al., 2015). Its secondary lineage arborizes in the adult superior lateral protocerebrum and lateral horn, and has a component that exits the brain to project to the ring gland (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] +comment: Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775 map the dorsal hemilineage of LHd2 to the dorsal hemilineage of DPLm2. Ring gland component previously thought to be a separate lineage (DPMl2) in Pereanu and Hartenstein (2006) (Wong et al., 2013). xref: VFB:FBbt_00100606 is_a: FBbt:00100745 ! neuroblast DPL property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158944,8 +158944,8 @@ property_value: IAO:0006011 FBbt:00050115 {xref="doi:10.1101/2020.06.12.148775"} [Term] id: FBbt:00100607 name: neuroblast DPLcv -def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +def: "Neuroblast that produces a lineage that joins a tract that curves under the mushroom body pedunculus (Pereanu and Hartenstein, 2006)." [FlyBase:FBrf0194268] +comment: 'DPLcv' only mentioned in one table, which is missing 'DPLpv', so this could be a typo. xref: VFB:FBbt_00100607 is_a: FBbt:00100745 ! neuroblast DPL property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -159870,6 +159870,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-12T12:09:59Z" xsd:dateTim id: FBbt:00100705 name: DPLcv lineage neuron def: "Neuron developing from the DPLcv neuroblast." [FlyBase:FBrf0194268] +comment: 'DPLcv' only mentioned in one table, which is missing 'DPLpv', so this could be a typo. xref: VFB:FBbt_00100705 property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string property_value: http://purl.org/dc/terms/date "2011-07-12T12:11:29Z" xsd:dateTime @@ -160230,7 +160231,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-13T02:13:42Z" xsd:dateTim [Term] id: FBbt:00100745 name: neuroblast DPL -def: "Neuroblast located in the dorsolateral aspect of the protocerebrum (Pereanu and Hartenstein, 2006)." [FlyBase:FBrf0194268] +def: "Neuroblast located in the dorsolateral protocerebrum during the larval stage (Pereanu and Hartenstein, 2006)." [FlyBase:FBrf0194268] synonym: "dorsoposterior lateral neuroblast" RELATED [] xref: VFB:FBbt_00100745 is_a: FBbt:00001334 ! protocerebral neuroblast From 78e5105358a6ea5bcc2f11852d3b20ba7208cb67 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Thu, 7 Dec 2023 12:36:38 +0000 Subject: [PATCH 3/3] DPMs --- src/ontology/fbbt-edit.obo | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/src/ontology/fbbt-edit.obo b/src/ontology/fbbt-edit.obo index 4e84d647f..840704a83 100644 --- a/src/ontology/fbbt-edit.obo +++ b/src/ontology/fbbt-edit.obo @@ -109756,14 +109756,15 @@ xref: VFB:FBbt_00050017 [Term] id: FBbt:00050018 name: neuroblast DM1 -def: "Type II neuroblast of the brain whose neuronal lineage enters the neuropil in a posterior medial location at the level of protocerebral bridge glomeruli 1-3 (Viktorin et al., 2011; Andrade et al., 2019)." [FlyBase:FBrf0214495, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0241389] +def: "Type II neuroblast of the brain whose neuronal lineage enters the neuropil in a posterior medial location at the level of protocerebral bridge glomeruli 1-3 (Viktorin et al., 2011; Andrade et al., 2019). Its primary lineage contributes to the fan-shaped body primordium (Riebli et al., 2013; Hartenstein et al., 2015). Its large secondary lineage produces numerous tracts with different trajectories, reaching many parts of the adult brain (Lovick et al., 2014; Ito et al., 2013; Yu et al., 2013)." [FlyBase:FBrf0214495, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0221883, FlyBase:FBrf0223329, FlyBase:FBrf0229672, FlyBase:FBrf0241389] subset: TL_lineage_clone synonym: "central complex neuroblast Z" EXACT [FlyBase:FBrf0236238] synonym: "FBP1" EXACT [FlyBase:FBrf0205148] -synonym: "neuroblast DPMm1" EXACT [FlyBase:FBrf0194268, FlyBase:FBrf0214495] +synonym: "neuroblast DPMm1" EXACT [FlyBase:FBrf0194268, FlyBase:FBrf0214495, FlyBase:FBrf0221883] xref: VFB:FBbt_00050018 is_a: FBbt:00001333 ! procephalic neuroblast is_a: FBbt:00100533 ! type II neuroblast +is_a: FBbt:00100744 ! neuroblast DPM [Term] id: FBbt:00050019 @@ -158616,7 +158617,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T11:51:47Z" xsd:dateTim [Term] id: FBbt:00100578 name: neuroblast DPMpl2 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412] +def: "Neuroblast that produces a primary lineage that enters the neuropil medial to the mushroom body calyx and joins the posterior longitudinal superior medial fascicle (loSM) (Hartenstein et al., 2015). In the adult, its secondary lineage follows the loSM, then continues medially to the fan-shaped body, where it forms wide-field arbors (Wong et al., 2013; Yu et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0229672] subset: TL_lineage_clone synonym: "neuroblast SIPp1" EXACT [doi:10.1101/2020.06.12.148775] xref: VFB:FBbt_00100578 @@ -158628,8 +158629,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:02:51Z" xsd:dateTim [Term] id: FBbt:00100579 name: neuroblast DPMpl3 -def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +def: "Neuroblast that produces neurons with cell bodies that are initially located close to those of the DPMpl1/2 lineages, but shift ventrally during metamorphosis (Wong et al., 2013). Its lineage projects along the medial equatorial fascicle (Wong et al., 2013; Hartenstein et al., 2015). In the adult it innervates several ventral brain regions (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] xref: VFB:FBbt_00100579 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158639,7 +158639,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:03:57Z" xsd:dateTim id: FBbt:00100580 name: neuroblast DPMpl4 def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +comment: Only shown in table of Pereanu and Hartenstein (2006) and not figure. Not mentioned in later papers from same group, so may not exist. xref: VFB:FBbt_00100580 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158678,8 +158678,7 @@ replaced_by: FBbt:00050018 [Term] id: FBbt:00100584 name: neuroblast DPMm2 -def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +def: "Neuroblast that forms a primary lineage that enters the neuropil at the dorsolateral protocerebral bridge and projects medially (Hartenstein et al., 2015). Its secondary lineage innervates adult posterior brain compartments and has a descending tract (Wong et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0223298, FlyBase:FBrf0229672] xref: VFB:FBbt_00100584 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158689,7 +158688,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:09:51Z" xsd:dateTim id: FBbt:00100585 name: neuroblast DPMm3 def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +comment: Not mentioned in later papers from same group, so may not exist. xref: VFB:FBbt_00100585 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158698,7 +158697,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:11:16Z" xsd:dateTim [Term] id: FBbt:00100586 name: neuroblast DPMl1 -def: "." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438] +def: "Neuroblast that produces a primary lineage that forms the dorsal posterior protecerebral tract (Hartenstein et al., 2015). Its secondary lineage has a descending projection as well as dense arbors in the adult vest (Wong et al., 2013; Lovick et al., 2013; Ito et al., 2013)." [FlyBase:FBrf0194268, FlyBase:FBrf0221412, FlyBase:FBrf0221438, FlyBase:FBrf0223298, FlyBase:FBrf0223329, FlyBase:FBrf0229672] comment: PSp3 mapped to DPMl1/2 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775, to DPMl1 in Hartenstein et al. (2017) - FBrf0234128. subset: TL_lineage_clone synonym: "neuroblast PSp3" EXACT [FlyBase:FBrf0234128] @@ -158712,7 +158711,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:12:29Z" xsd:dateTim id: FBbt:00100587 name: neuroblast DPMl2 def: "." [FlyBase:FBrf0194268] -comment: PSp3 mapped to DPMl1/2 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775, to DPMl1 in Hartenstein et al. (2017) - FBrf0234128. +comment: PSp3 mapped to DPMl1/2 in Eckstein et al. (2020) - doi:10.1101/2020.06.12.148775, to DPMl1 in Hartenstein et al. (2017) - FBrf0234128. Wong et al. (2013) say that this was incorrectly assigned as a distinct lineage in Pereanu and Hartenstein (2006), but seems to still be considered to be a lineage by same group in Hartenstein et al. (2015). xref: VFB:FBbt_00100587 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158722,7 +158721,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:13:45Z" xsd:dateTim id: FBbt:00100588 name: neuroblast DPMl3 def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +comment: Renamed to DPLc5 in Lovick et al. (2013) - FBrf0223329. xref: VFB:FBbt_00100588 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -158732,7 +158731,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-11T12:14:44Z" xsd:dateTim id: FBbt:00100589 name: neuroblast DPMl4 def: "." [FlyBase:FBrf0194268] -comment: The existence of this neuroblast is inferred from lineage data (Pereanu and Hartenstein, 2006). This paper studies secondary neuroblast divisions. Although all of these lineages will correspond to a lineage from a known primary neuroblast lineage, only some will correspond to lineages from the secondary neuroblast division. +comment: This neuroblast/lineage is not refered to in later papers from the same group, so may not exist. xref: VFB:FBbt_00100589 is_a: FBbt:00100744 ! neuroblast DPM property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string @@ -160222,7 +160221,7 @@ property_value: http://purl.org/dc/terms/date "2011-07-13T02:09:27Z" xsd:dateTim [Term] id: FBbt:00100744 name: neuroblast DPM -def: "Neuroblast located in the dorsoposterior medial protocerebrum (Pereanu and Hartenstein, 2006)." [FlyBase:FBrf0194268] +def: "Neuroblast located in the dorsoposterior medial protocerebrum during the larval stage (Pereanu and Hartenstein, 2006)." [FlyBase:FBrf0194268] xref: VFB:FBbt_00100744 is_a: FBbt:00001334 ! protocerebral neuroblast property_value: http://purl.org/dc/elements/1.1/contributor "FBC:sr544" xsd:string