From 231b871f68afe9515f667dac01f598046b61d380 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 12 Jan 2016 21:23:36 -0800 Subject: [PATCH] NTs: main, accessor nidamental glands; NT: circumoral appendage bud --- src/ontology/Makefile | 4 +- src/ontology/ceph.obo | 22 +++- src/ontology/ceph.owl | 257 ++++++++++++++++++++++++------------------ 3 files changed, 171 insertions(+), 112 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 998b776..0a1dad7 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -8,8 +8,8 @@ RELEASE = $(OBO)/ceph/releases/`date +%Y-%m-%d` # # To make a release, type 'make release' in this directory -build: ceph.obo minidiff -release: ceph.obo diff +build: ceph.obo +release: ceph.obo test: ceph.obo diff --git a/src/ontology/ceph.obo b/src/ontology/ceph.obo index 7e7361c..de46e37 100644 --- a/src/ontology/ceph.obo +++ b/src/ontology/ceph.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2015-03-15 +data-version: releases/2016-01-12 synonymtypedef: acronym "acronym" broad synonymtypedef: anamorph "anamorph" related synonymtypedef: blast_name "blast name" related @@ -38,6 +38,12 @@ is_a: UBERON:0000061 ! anatomical structure created_by: cjm creation_date: 2011-01-30T08:15:10Z +[Term] +id: CEPH:0000001 +name: accessory nidamental gland +def: "The basic structural unit is a tubule composed of a single layer of epithelial cells containing ordered arrays of rough endoplasmic reticulum and a lumenal surface covered with microvilli, cilia, and structural specialization presumed to be involved in secretion." [http://www.ncbi.nlm.nih.gov/pubmed/906013] +is_a: CEPH:0000175 ! nidamental gland + [Term] id: CEPH:0000002 name: cephalopod eye @@ -46,6 +52,11 @@ is_a: UBERON:0000970 ! eye created_by: cjm creation_date: 2011-01-30T08:21:37Z +[Term] +id: CEPH:0000003 +name: circumoral appendage bud +is_a: UBERON:0005423 ! developing anatomical structure + [Term] id: CEPH:0000004 name: accessory gland complex @@ -67,6 +78,11 @@ name: adult stage def: "A female that has mature eggs (these are frequently stored in the oviducts), or a male that has produced spermatophores (these are stored in Needham's sac)." [http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587] is_a: UBERON:0000105 ! life cycle stage +[Term] +id: CEPH:0000007 +name: main nidamental gland +is_a: CEPH:0000175 ! nidamental gland + [Term] id: CEPH:0000009 name: anal flap @@ -1021,9 +1037,10 @@ relationship: part_of CEPH:0001037 ! renal sac [Term] id: CEPH:0000175 name: nidamental gland -def: "Large glandular structures found in decapodiforms and Nautilus that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses." [http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587] +def: "Large glandular structures found in decapodiforms and Nautilus that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses." [http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587] is_a: UBERON:0002530 ! gland relationship: RO:0001025 UBERON:0006580 ! located in mantle cavity +property_value: seeAlso Nidamental:gland [Term] id: CEPH:0000176 @@ -1820,6 +1837,7 @@ def: "Any of the numerous arms or tentacles that arise from the head and surroun synonym: "arm crown" RELATED [] synonym: "head appendage" RELATED [] is_a: UBERON:0000026 ! appendage +relationship: RO:0002202 CEPH:0000003 ! develops from circumoral appendage bud [Term] id: CEPH:0000309 diff --git a/src/ontology/ceph.owl b/src/ontology/ceph.owl index fe6714b..7cc4f4f 100644 --- a/src/ontology/ceph.owl +++ b/src/ontology/ceph.owl @@ -20,7 +20,7 @@ - + @@ -421,6 +421,22 @@ + + + + accessory nidamental gland + + The basic structural unit is a tubule composed of a single layer of epithelial cells containing ordered arrays of rough endoplasmic reticulum and a lumenal surface covered with microvilli, cilia, and structural specialization presumed to be involved in secretion. + + + The basic structural unit is a tubule composed of a single layer of epithelial cells containing ordered arrays of rough endoplasmic reticulum and a lumenal surface covered with microvilli, cilia, and structural specialization presumed to be involved in secretion. + + + + + + + @@ -433,6 +449,15 @@ + + + + circumoral appendage bud + + + + + @@ -441,14 +466,14 @@ - - + + - - + + The glandular complex in cirrates that forms sperm packets and is a counterpart of the spermatophore-forming complex of other cephalopods. @@ -494,6 +519,15 @@ + + + + main nidamental gland + + + + + @@ -790,14 +824,14 @@ - - + + - - + + The anterior-most part of the brain located ventral to the esophagus. The large axial nerve cords that run down the centers of the arms connect to this lobe. In octopods this lobe is fused with the rest of the subesophageal mass while in decapodiforms and <strong>Vampyroteuthis</strong> it is separate from the remaining brain. @@ -861,18 +895,18 @@ Photophores located on the arms. photophore at base of gill[http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015]l - - Photophores located on the arms. - http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587 - - - http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015 photophore at base of gill[http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015]l + + Photophores located on the arms. + http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587 + + + @@ -1006,7 +1040,7 @@ - + @@ -1018,7 +1052,7 @@ - + The muscular membrane that connects the buccal supports and together with the supports, forms the buccal crown. The pigmentation of the buccal membrane often differs from that of the adjacent oral surfaces of the arms. @@ -1140,14 +1174,14 @@ - - + + - - + + The conical papilla of the end-organ of the hectocotylus in many incirrate octopods. It is located at the distal termination of the sperm groove and usually lies adjacent to the last arm sucker. @@ -1541,14 +1575,14 @@ - - + + - - + + Lateral portions of the gladius that are continuous posteriorly with the primary conus or its remnant and laterally with the edges of the vanes. @@ -1630,14 +1664,14 @@ - - + + - - + + Expansion (i.e. a broading or a side pocket) of the esophagus for storing food. Present in <strong>Nautilus</strong> and most octopodiforms. @@ -1848,14 +1882,14 @@ - - + + - - + + Outpockets of the ducts leading from the digestive gland that are covered with glandular epithelium. @@ -2314,14 +2348,14 @@ - - + + - - + + The ventral, muscular tube through which water is expelled from the mantle cavity. The funnel is thought to have evolved from the molluscan foot. @@ -2509,14 +2543,14 @@ - - + + - - + + The chitinous remnant of the shell in many decapodiforms and <strong>Vampyroteuthis</strong>. It is generally feather-shaped and lies in the dorsal mid-line of the body along the full length of the mantle. The gladius lies within the shell sac which secretes it. @@ -2589,13 +2623,13 @@ - + - + . @@ -2692,14 +2726,14 @@ - - + + - - + + Horny structure that looks like a single claw and is derived from the inner sucker ring in some decapodiforms. Hooks may be found on the arms and/or tentacular clubs of squid. The relative advantage of hooks vs toothed rings is uncertain. @@ -3222,14 +3256,14 @@ - - + + - - + + In males, the large storage sac for spermatophores that is an expanded region of the genital duct at the base of the penis. @@ -3278,10 +3312,11 @@ - Large glandular structures found in decapodiforms and <strong>Nautilus</strong> that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses. + Large glandular structures found in decapodiforms and Nautilus that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses. + - Large glandular structures found in decapodiforms and <strong>Nautilus</strong> that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses. + Large glandular structures found in decapodiforms and Nautilus that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587 @@ -3575,6 +3610,12 @@ The long, muscular end of the male gonoduct that assists in transfering spermatophores to the female. Apparently, in species with a hectocotylus, the penis transfers spermatophores to the hectocotylus which in turn transfers them to the female. In species without a hectocotylus, the penis is often greatly elongate, capable of extending beyond the mantle cavity and can, apparently, transfer spermatophores directly to the female. terminal organ + + Wikipedia + + + + The long, muscular end of the male gonoduct that assists in transfering spermatophores to the female. Apparently, in species with a hectocotylus, the penis transfers spermatophores to the hectocotylus which in turn transfers them to the female. In species without a hectocotylus, the penis is often greatly elongate, capable of extending beyond the mantle cavity and can, apparently, transfer spermatophores directly to the female. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587 @@ -3588,12 +3629,6 @@ - - Wikipedia - - - - @@ -3775,18 +3810,18 @@ Membranes, generally supported by trabeculae, that form lateral borders along the oral surfaces of the arms and tentacular clubs in decapodiforms. A thin fold of integument along lateral angles of oral surface of arms and clubs lateral to suckers usually supported by trabeculae - - http://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdf - A thin fold of integument along lateral angles of oral surface of arms and clubs lateral to suckers usually supported by trabeculae - - - Membranes, generally supported by trabeculae, that form lateral borders along the oral surfaces of the arms and tentacular clubs in decapodiforms. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587 + + http://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdf + A thin fold of integument along lateral angles of oral surface of arms and clubs lateral to suckers usually supported by trabeculae + + + @@ -4318,14 +4353,14 @@ - - + + - - + + Region of the tentacle proximal to the club. @@ -4625,10 +4660,11 @@ Elongate 4th circumoral appendage of cuttlefish and squids used to capture prey. Divided into proximal stalk and distal club. + Modified 4th pair of appendages in decapodiforms that are capable of considerable extension and contraction. Although the tentacles are derived evolutionarily from the 4th pair of arms, the term, "arms IV"; is reserved for the subsequent arm pair, the ventral arms, which are evolutionarily the 5th pair of arms. Each tentacle consist of a proximal stalk usually devoid of suckers, and a distal club armed with suckers and occasionally hooks. Wikipedia:Cephalopod_limb - arm + http://tolweb.org/accessory/Composite_Squid?acc_id=1936 - + Wikipedia:Cephalopod_limb @@ -4643,11 +4679,10 @@ - Modified 4th pair of appendages in decapodiforms that are capable of considerable extension and contraction. Although the tentacles are derived evolutionarily from the 4th pair of arms, the term, "arms IV"; is reserved for the subsequent arm pair, the ventral arms, which are evolutionarily the 5th pair of arms. Each tentacle consist of a proximal stalk usually devoid of suckers, and a distal club armed with suckers and occasionally hooks. Wikipedia:Cephalopod_limb - http://tolweb.org/accessory/Composite_Squid?acc_id=1936 + arm - + @@ -4872,14 +4907,14 @@ - - + + - - + + Broad, lateral portions of the gladius that arise from the rhachis. @@ -4951,32 +4986,32 @@ - - + + - - + + A concentration of digestive organs that sometimes includes reproductive organs as well. In cranchiid squids the visceral nucleus is especially distinct: the small, spindle-shaped digestive gland contains the ink sac and is adjacent to the stomach and caecum and associated structures (eg, digestive gland duct appendages, renal appendages). In most cephalopods the concentration of these structures is not so extensive but whenever a concentration exists, a visceral nucleus is present. BTO:0001448 visceral hump - - BTO:0001448 - visceral hump - - - A concentration of digestive organs that sometimes includes reproductive organs as well. In cranchiid squids the visceral nucleus is especially distinct: the small, spindle-shaped digestive gland contains the ink sac and is adjacent to the stomach and caecum and associated structures (eg, digestive gland duct appendages, renal appendages). In most cephalopods the concentration of these structures is not so extensive but whenever a concentration exists, a visceral nucleus is present. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587 + + BTO:0001448 + visceral hump + + + @@ -5262,13 +5297,13 @@ - + - + Large nerve bundles that run from the optic lobe to the eye. @@ -5513,6 +5548,12 @@ circumoral appendage + + + + + + arm crown head appendage Any of the numerous arms or tentacles that arise from the head and surround the mouth of a cephalopod @@ -5598,14 +5639,14 @@ - - + + - - + + Collection of chromatophores that produces species-specific patterns in discrete regions @@ -5667,8 +5708,8 @@ - - + + @@ -5679,13 +5720,19 @@ - - + + found in fossil teuthoids The phragmocone is the chambered portion of the shell of a cephalopod. It is divided by septa into camerae. + + http://en.wikipedia.org/wiki/Phragmocone + The phragmocone is the chambered portion of the shell of a cephalopod. It is divided by septa into camerae. + + + http://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdf found in fossil teuthoids @@ -5703,12 +5750,6 @@ - - http://en.wikipedia.org/wiki/Phragmocone - The phragmocone is the chambered portion of the shell of a cephalopod. It is divided by septa into camerae. - - - @@ -6282,13 +6323,13 @@ - + - + @@ -14264,13 +14305,13 @@ - + - +