Worm Phenotype (WP): neuron development variant

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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
Mouse Phenotype (MP) Ontology (MP)
MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
Worm Phenotype (WP) Ontology (WP)
WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
Yeast Phenotype (YP) Ontology (YP)
Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
Fly Phenotype (FP) Ontology (FP)
FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
Fly Anatomy (FA) Ontology (FA)
FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
Zebrafish Anatomy (ZA) Ontology (ZA)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
Arabidopsis Plant Ontology (AP) Ontology (AP)
As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
Enzyme Commission (EC) Ontology (EC)
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

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Root: WP Hierarchy (worm phenotype from Wormbase Release WS226)

Shortest distance to current term (+ for parents, - for children) WP term [WP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + 4: Variant [WBPhenotype:0000886] <2>

+ + + 3: physiology variant [WBPhenotype:0000519] <14> (510|587) (510|248|68)

+ + 2: development variant [WBPhenotype:0000518] <6> (508|585) (508|248|68)

+ 1: cell development variant [WBPhenotype:0000529] <17> (119|124) (119|47|12)

0: neuron development variant [WBPhenotype:0000816] <6> (29|28) (30|11|4)

- 1: synaptic transmission variant [WBPhenotype:0000584] <7> (6|5) (6|2|1)

- 1: neurite development variant [WBPhenotype:0000944] <5> (6|8) (6|4|3)

- 1: neuronal outgrowth variant [WBPhenotype:0000572] <4> (20|16) (21|8|4)

- 1: chemosensory neuron development variant [WBPhenotype:0000878] (0|0) (0|0|0)

- 1: neuron cell body absent misplaced [WBPhenotype:0001333] (1|1) (1|0|0)

- 1: neuronal ion channel clustering defective [WBPhenotype:0001786] (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Immunoglobulin	0.00000000001641	Direct
Fibronectin type III	0.00000002039	Direct
Sema domain	0.00000002734	Direct
GTPase activation domain, GAP	0.00000008234	Direct
Plexin repeat	0.000003324	Direct
Concanavalin A-like lectins/glucanases	0.00006885	Direct
Homeodomain-like	0.0001394	Direct
RNA-binding domain, RBD	0.0001688	Direct
Frizzled cysteine-rich domain	0.001063	Inherited
Troponin coil-coiled subunits	0.001063	Inherited
Cadherin-like	0.001252	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.001762	Inherited
SAM/Pointed domain	0.002814	Inherited
Tubulin nucleotide-binding domain-like	0.003833	Inherited
PDZ domain-like	0.007982	Inherited
Tubulin C-terminal domain-like	0.008871	Inherited
Protein kinase-like (PK-like)	0.01487	Inherited
P-loop containing nucleoside triphosphate hydrolases	0.02109	Inherited
dsRNA-binding domain-like	0.02636	Inherited
Cysteine-rich domain	0.03006	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.0335	Inherited
HLH, helix-loop-helix DNA-binding domain	0.03747	Inherited
Nicotinic receptor ligand binding domain-like	0.06519	Inherited
Calponin-homology domain, CH-domain	0.07336	Inherited
Eukaryotic type KH-domain (KH-domain type I)	0.07336	Inherited
PH domain-like	0.08967	Inherited
Growth factor receptor domain	0.1457	Inherited
SMAD/FHA domain	0.2809	Inherited
EGF/Laminin	0.3481	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Troponin I	0	Direct
Fibronectin type III	0.00000006031	Direct
BCR-homology GTPase activation domain (BH-domain)	0.0000001207	Direct
Sema domain	0.000001377	Direct
I set domains	0.000001952	Direct
Plexin repeat	0.000007644	Direct
Homeodomain	0.00002973	Direct
Cadherin	0.0003046	Direct
Frizzled cysteine-rich domain	0.001272	Inherited
Laminin G-like module	0.001608	Inherited
Canonical RBD	0.002454	Inherited
Synaptotagmin-like (S variant)	0.002871	Inherited
Tandem AAA-ATPase domain	0.004314	Inherited
Tubulin, GTPase domain	0.004923	Inherited
Motor proteins	0.008749	Inherited
Tubulin, C-terminal domain	0.01136	Inherited
Protein kinases, catalytic subunit	0.01591	Inherited
Pleckstrin-homology domain (PH domain)	0.01747	Inherited
FHA domain	0.01984	Inherited
PDZ domain	0.04031	Inherited
Double-stranded RNA-binding domain (dsRBD)	0.04607	Inherited
HLH, helix-loop-helix DNA-binding domain	0.05386	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.06947	Inherited
Calponin-homology domain, CH-domain	0.08785	Inherited
Eukaryotic type KH-domain (KH-domain type I)	0.08785	Inherited
Nicotinic receptor ligand binding domain-like	0.1024	Inherited
Growth factor receptor domain	0.1319	Inherited
G proteins	0.2905	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Immunoglobulin	0.00000000001296	Direct
Fibronectin type III	0.00000001628	Direct
Sema domain	0.00000002184	Direct
GTPase activation domain, GAP	0.00000006595	Direct
Plexin repeat	0.000002699	Direct
Concanavalin A-like lectins/glucanases	0.00005632	Direct
Homeodomain-like	0.0001144	Direct
RNA-binding domain, RBD	0.0001386	Direct
Troponin coil-coiled subunits	0.0008848	Direct
Frizzled cysteine-rich domain	0.0008848	Direct
Cadherin-like	0.001044	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.001475	Inherited
SAM/Pointed domain	0.002373	Inherited
Tubulin nucleotide-binding domain-like	0.003247	Inherited
PDZ domain-like	0.00683	Inherited
Tubulin C-terminal domain-like	0.007611	Inherited
Protein kinase-like (PK-like)	0.01288	Inherited
P-loop containing nucleoside triphosphate hydrolases	0.01837	Inherited
dsRNA-binding domain-like	0.02308	Inherited
Cysteine-rich domain	0.02639	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.02947	Inherited
HLH, helix-loop-helix DNA-binding domain	0.03302	Inherited
Nicotinic receptor ligand binding domain-like	0.05815	Inherited
Calponin-homology domain, CH-domain	0.06564	Inherited
Eukaryotic type KH-domain (KH-domain type I)	0.06564	Inherited
PH domain-like	0.08067	Inherited
BAR/IMD domain-like	0.09634	Inherited
Growth factor receptor domain	0.1328	Inherited
SMAD/FHA domain	0.2623	Inherited
EGF/Laminin	0.3281	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.000000009173	Direct
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.000001913	Direct
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.0000103	Direct
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.0008848	Direct
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.0008848	Direct
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0.003247	Inherited
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat	0.003967	Inherited
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.006265	Inherited
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.02947	Inherited
81296,81296 81296 - E set domains 81296 - E set domains	0.03209	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.474	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.00000349	Direct
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.0000103	Direct
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.0001937	Direct
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.0008848	Direct

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Worm Phenotype (WP): neuron development variant

Superfamily

Family

Supra-domain (including individual superfamily)