Worm Phenotype (WP): muscle system physiology 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)

+ + + 3: Variant [WBPhenotype:0000886] <2>

+ + 2: physiology variant [WBPhenotype:0000519] <14> (510|587) (510|248|68)

+ 1: organ system physiology variant [WBPhenotype:0000575] <8> (445|529) (445|229|63)

0: muscle system physiology variant [WBPhenotype:0000611] <4> (27|29) (29|14|5)

- 1: muscle cell physiology variant [WBPhenotype:0000990] <8> (21|22) (22|13|4)

- 1: muscle dystrophy [WBPhenotype:0000548] <2> (5|4) (5|0|0)

- 1: body wall muscle contraction abnormal [WBPhenotype:0000153] (0|0) (0|0|0)

- 1: head muscle contraction variant [WBPhenotype:0000423] (0|0) (0|0|0)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
PH domain-like	0	Direct
SH3-domain	0.0000000000008485	Direct
SH2 domain	0.00000000002824	Direct
PLC-like phosphodiesterases	0.00000001558	Direct
Frizzled cysteine-rich domain	0.00000002057	Direct
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00000004153	Direct
Growth factor receptor domain	0.0000002399	Direct
Ubiquitin-like	0.0000006786	Direct
Second domain of FERM	0.000004214	Direct
Protein kinase-like (PK-like)	0.000004275	Direct
Tropomyosin	0.000007687	Direct
Spectrin repeat	0.000007687	Direct
Calponin-homology domain, CH-domain	0.000009303	Direct
EF-hand	0.0000419	Direct
EGF/Laminin	0.00008153	Direct
Myosin rod fragments	0.00008995	Direct
GTPase activation domain, GAP	0.0001293	Direct
Lamin A/C globular tail domain	0.0002054	Direct
Intermediate filament protein, coiled coil region	0.0002196	Direct
PDZ domain-like	0.0002396	Direct
Cysteine-rich domain	0.0002454	Direct
cAMP-binding domain-like	0.000602	Direct
DBL homology domain (DH-domain)	0.001624	Inherited
Voltage-gated potassium channels	0.002167	Inherited
(Phosphotyrosine protein) phosphatases II	0.002533	Inherited
Actin-like ATPase domain	0.003474	Inherited
"Winged helix" DNA-binding domain	0.2707	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Mammalian PLC	0	Direct
SH3-domain	0.00000000002327	Direct
PLC-like (P variant)	0.000000000181	Direct
Pleckstrin-homology domain (PH domain)	0.0000000005112	Direct
SH2 domain	0.0000000005877	Direct
Frizzled cysteine-rich domain	0.00000004976	Direct
EF-hand modules in multidomain proteins	0.00000004976	Direct
LIM domain	0.0000002652	Direct
Laminin-type module	0.0000002867	Direct
PDZ domain	0.000006117	Direct
DEP domain	0.00000796	Direct
Second domain of FERM	0.000008246	Direct
Third domain of FERM	0.0000103	Direct
Spectrin repeat	0.0000103	Direct
Tropomyosin	0.00001822	Direct
First domain of FERM	0.00002282	Direct
Calponin-homology domain, CH-domain	0.00003269	Direct
Protein kinases, catalytic subunit	0.00003967	Direct
Phosphotyrosine-binding domain (PTB)	0.00004733	Direct
Growth factor receptor domain	0.0001032	Direct
Lamin A/C globular tail domain	0.0001581	Direct
Myosin rod fragments	0.0001696	Direct
Intermediate filament protein, coiled coil region	0.0004111	Direct
BCR-homology GTPase activation domain (BH-domain)	0.0006597	Direct
cAMP-binding domain	0.0008287	Direct
Actin/HSP70	0.001082	Inherited
DBL homology domain (DH-domain)	0.00299	Inherited
I set domains	0.003669	Inherited
Voltage-gated potassium channels	0.01475	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)
PH domain-like	0	Direct
SH3-domain	0.000000000000668	Direct
SH2 domain	0.00000000002232	Direct
PLC-like phosphodiesterases	0.00000001242	Direct
Frizzled cysteine-rich domain	0.00000001642	Direct
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00000003322	Direct
Growth factor receptor domain	0.0000001928	Direct
Ubiquitin-like	0.0000005476	Direct
Second domain of FERM	0.000003423	Direct
Protein kinase-like (PK-like)	0.000003473	Direct
Tropomyosin	0.000006252	Direct
Spectrin repeat	0.000006252	Direct
Calponin-homology domain, CH-domain	0.000007567	Direct
EF-hand	0.00003424	Direct
EGF/Laminin	0.00006673	Direct
Myosin rod fragments	0.00007368	Direct
GTPase activation domain, GAP	0.0001061	Direct
Lamin A/C globular tail domain	0.0001688	Direct
Intermediate filament protein, coiled coil region	0.0001805	Direct
PDZ domain-like	0.000197	Direct
Cysteine-rich domain	0.0002018	Direct
cAMP-binding domain-like	0.0004987	Direct
Fibronectin type III	0.0008674	Direct
DBL homology domain (DH-domain)	0.001358	Inherited
Voltage-gated potassium channels	0.00182	Inherited
(Phosphotyrosine protein) phosphatases II	0.002133	Inherited
Actin-like ATPase domain	0.002939	Inherited
BAR/IMD domain-like	0.006099	Inherited
"Winged helix" DNA-binding domain	0.2524	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	Direct
50729,47473 50729 - PH domain-like 47473 - EF-hand	0	Direct
51695,49562 51695 - PLC-like phosphodiesterases 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0	Direct
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.0000000003103	Direct
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0000004929	Direct
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	0.000000528	Direct
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.0000007077	Direct
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.0000164	Direct
50044,50044 50044 - SH3-domain 50044 - SH3-domain	0.00002191	Direct
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain	0.00002191	Direct
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.00002191	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.00002191	Direct
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.001535	Inherited
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.004242	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	Direct
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.0000000002876	Direct
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.000009746	Direct
54236,47031,50729 54236 - Ubiquitin-like 47031 - Second domain of FERM 50729 - PH domain-like	0.0000104	Direct
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.00003614	Direct

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

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Worm Phenotype (WP): muscle system physiology variant

Superfamily

Family

Supra-domain (including individual superfamily)