Worm Phenotype (WP): basement membrane remodeling 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: pericellular component development variant [WBPhenotype:0000200] <4> (31|39) (31|15|5)

0: basement membrane remodeling variant [WBPhenotype:0002065] <1> (25|35) (25|15|5)

- 1: basement membrane gap expansion variant [WBPhenotype:0002066] (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
BPTI-like	0	Direct
Blood coagulation inhibitor (disintegrin)	0	Direct
Zn-dependent exopeptidases	0	Direct
PGBD-like	0	Direct
Carboxypeptidase regulatory domain-like	0	Direct
Acid proteases	8.972e-16	Direct
Cysteine proteinases	0.000000000000005821	Direct
alpha/beta-Hydrolases	0.00000000000003216	Direct
Protease propeptides/inhibitors	0.000000000001058	Direct
Creatinase/aminopeptidase	0.00000000003315	Direct
Trypsin-like serine proteases	0.0000000001914	Direct
TSP-1 type 1 repeat	0.00000001334	Direct
Bacterial exopeptidase dimerisation domain	0.00000004279	Direct
Subtilisin-like	0.00000004279	Direct
Serine protease inhibitors	0.00000004304	Direct
Metalloproteases ("zincins"), catalytic domain	0.00000006089	Direct
Hemopexin-like domain	0.0000002455	Direct
Spermadhesin, CUB domain	0.0000005036	Direct
LuxS/MPP-like metallohydrolase	0.0000008527	Direct
Integrin domains	0.000001567	Direct
Serpins	0.000004186	Direct
Thyroglobulin type-1 domain	0.0000212	Direct
beta-lactamase/transpeptidase-like	0.00002572	Direct
Leukotriene A4 hydrolase N-terminal domain	0.0001238	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.0002099	Direct

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Matrix metalloproteases, catalytic domain	0	Direct
DPP6 catalytic domain-like	0	Direct
Blood coagulation inhibitor (disintegrin)	0	Direct
DPP6 N-terminal domain-like	0	Direct
Acylamino-acid-releasing enzyme, C-terminal donain	0	Direct
Astacin	0	Direct
Carboxypeptidase regulatory domain	0	Direct
Neutral endopeptidase (neprilysin)	0	Direct
Proprotein convertase P-domain	0	Direct
Methionine aminopeptidase, insert domain	0	Direct
Small Kunitz-type inhibitors & BPTI-like toxins	0	Direct
Papain-like	0	Direct
Integrin domains	0	Direct
Pepsin-like	6.263e-16	Direct
Pancreatic carboxypeptidases	0.0000000000003192	Direct
Reprolysin-like	0.000000000004529	Direct
Bacterial dinuclear zinc exopeptidases	0.00000000003936	Direct
Creatinase/aminopeptidase	0.0000000001899	Direct
Serine carboxypeptidase-like	0.000000001028	Direct
TSP-1 type 1 repeat	0.0000001126	Direct
Subtilases	0.0000001134	Direct
Bacterial exopeptidase dimerisation domain	0.0000001134	Direct
Hemopexin-like domain	0.0000006487	Direct
Pancreatic carboxypeptidase, activation domain	0.000002166	Direct
MPP-like	0.000002831	Direct
Eukaryotic proteases	0.000005517	Direct
Serpins	0.000008496	Direct
beta-Lactamase/D-ala carboxypeptidase	0.00001187	Direct
ATI-like	0.00001187	Direct
Spermadhesin, CUB domain	0.00001842	Direct
Thyroglobulin type-1 domain	0.00004337	Direct
Gamma-glutamyltranspeptidase-like	0.00004337	Direct
Acetylcholinesterase-like	0.0001114	Direct
Leukotriene A4 hydrolase N-terminal domain	0.0005046	Direct
Leukotriene A4 hydrolase catalytic domain	0.0005046	Direct

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)
Zn-dependent exopeptidases	0	Direct
PGBD-like	0	Direct
BPTI-like	0	Direct
Carboxypeptidase regulatory domain-like	0	Direct
Blood coagulation inhibitor (disintegrin)	0	Direct
Acid proteases	7.031e-16	Direct
Cysteine proteinases	0.000000000000004563	Direct
alpha/beta-Hydrolases	0.00000000000002524	Direct
Protease propeptides/inhibitors	0.0000000000008332	Direct
Creatinase/aminopeptidase	0.0000000000262	Direct
Trypsin-like serine proteases	0.0000000001516	Direct
TSP-1 type 1 repeat	0.00000001064	Direct
Bacterial exopeptidase dimerisation domain	0.00000003423	Direct
Subtilisin-like	0.00000003423	Direct
Serine protease inhibitors	0.00000003443	Direct
Metalloproteases ("zincins"), catalytic domain	0.00000004874	Direct
Hemopexin-like domain	0.0000001974	Direct
Spermadhesin, CUB domain	0.0000004058	Direct
LuxS/MPP-like metallohydrolase	0.0000006886	Direct
Integrin domains	0.000001268	Direct
Serpins	0.000003401	Direct
Thyroglobulin type-1 domain	0.00001728	Direct
beta-lactamase/transpeptidase-like	0.00002099	Direct
Leukotriene A4 hydrolase N-terminal domain	0.0001015	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.0001725	Direct

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
55486,49854 55486 - Metalloproteases ("zincins"), catalytic domain 49854 - Spermadhesin, CUB domain	0	Direct
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	Direct
54897,52743 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like	0	Direct
53187,49464 53187 - Zn-dependent exopeptidases 49464 - Carboxypeptidase regulatory domain-like	0	Direct
55920,46785 55920 - Creatinase/aminopeptidase 46785 - "Winged helix" DNA-binding domain	0	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0	Direct
52743,49785 52743 - Subtilisin-like 49785 - Galactose-binding domain-like	0	Direct
55486,57552 55486 - Metalloproteases ("zincins"), catalytic domain 57552 - Blood coagulation inhibitor (disintegrin)	0	Direct
57362,57362 57362 - BPTI-like 57362 - BPTI-like	0.00000000000001613	Direct
82171,53474 82171 - DPP6 N-terminal domain-like 53474 - alpha/beta-Hydrolases	0.0000000009032	Direct
82895,82895 82895 - TSP-1 type 1 repeat 82895 - TSP-1 type 1 repeat	0.000000002596	Direct
54897,53187 54897 - Protease propeptides/inhibitors 53187 - Zn-dependent exopeptidases	0.00000002372	Direct
53187,55031 53187 - Zn-dependent exopeptidases 55031 - Bacterial exopeptidase dimerisation domain	0.00000003423	Direct
63411,63411 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase	0.0000006886	Direct
63737,55486 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain	0.00004973	Direct

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57362,57362,57362 57362 - BPTI-like 57362 - BPTI-like 57362 - BPTI-like	0	Direct
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0	Direct
54897,52743,49785 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like 49785 - Galactose-binding domain-like	0	Direct
82895,82895,82895 82895 - TSP-1 type 1 repeat 82895 - TSP-1 type 1 repeat 82895 - TSP-1 type 1 repeat	0.000000002596	Direct
63411,63411,63411 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase	0.000006031	Direct

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

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Worm Phenotype (WP): basement membrane remodeling variant

Superfamily

Family

Supra-domain (including individual superfamily)