Worm Phenotype (WP): meiotic progression during oogenesis 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)

+ + + + + + + 7: Variant [WBPhenotype:0000886] <2>

+ + + + + + 6: physiology variant [WBPhenotype:0000519] <14> (510|587) (510|248|68)

+ + + + + 5: development variant [WBPhenotype:0000518] <6> (508|585) (508|248|68)

+ + + + 4: cell development variant [WBPhenotype:0000529] <17> (119|124) (119|47|12)

+ + + 3: gametogenesis variant [WBPhenotype:0000774] <2> (57|57) (58|22|4)

+ + 2: germ cell development variant [WBPhenotype:0000812] <7> (54|57) (55|22|4)

+ + 2: germ cell differentiation variant [WBPhenotype:0000894] <3> (38|40) (38|15|2)

+ 1: oogenesis variant [WBPhenotype:0000186] <5> (33|34) (33|14|2)

0: meiotic progression during oogenesis variant [WBPhenotype:0000313] <2> (26|28) (26|12|2)

- 1: meiotic progression prophase variant [WBPhenotype:0001824] <4> (24|23) (24|11|2)

- 1: oocyte meiotic maturation variant [WBPhenotype:0000105] <1> (1|2) (1|1|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Skp1 dimerisation domain-like	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
GroEL-intermediate domain like	0.0000000001009	Direct
GroEL equatorial domain-like	0.0000000001009	Direct
GroEL apical domain-like	0.0000000004842	Direct
Sm-like ribonucleoproteins	0.00000001465	Direct
Translation proteins SH3-like domain	0.0000002022	Direct
Nucleic acid-binding proteins	0.000004856	Direct
L30e-like	0.00002306	Direct
F1F0 ATP synthase subunit C	0.00002757	Direct
Ribosomal proteins S24e, L23 and L15e	0.00002757	Direct
S15/NS1 RNA-binding domain	0.00002757	Direct
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.00007681	Direct
Translational machinery components	0.00007791	Direct
"Winged helix" DNA-binding domain	0.0001727	Direct
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.0005511	Direct
Nucleotidylyl transferase	0.005528	Inherited
Histone-fold	0.03	Inherited
POZ domain	0.03009	Inherited
CCCH zinc finger	0.03359	Inherited
Class II aaRS and biotin synthetases	0.2513	Inherited
Translation proteins	0.2513	Inherited
Ribosomal protein S5 domain 2-like	0.3146	Inherited
Protein kinase-like (PK-like)	0.8073	Inherited
SNARE-like	0.8111	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Group II chaperonin (CCT, TRIC), intermediate domain	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Skp1 dimerisation domain-like	0	Direct
Group II chaperonin (CCT, TRIC), ATPase domain	0.00000000004619	Direct
Proteasome subunits	0.00000000007897	Direct
Group II chaperonin (CCT, TRIC), apical domain	0.0000000003959	Direct
Sm motif of small nuclear ribonucleoproteins, SNRNP	0.000001286	Direct
RecA protein-like (ATPase-domain)	0.00000269	Direct
Anticodon-binding domain	0.00001009	Direct
Translational machinery components	0.00002229	Direct
Extended AAA-ATPase domain	0.00002532	Direct
L30e/L7ae ribosomal proteins	0.00004701	Direct
F1F0 ATP synthase subunit C	0.00004701	Direct
Pumilio repeat	0.00008985	Direct
Cold shock DNA-binding domain-like	0.0001121	Direct
Elongation factors	0.0002188	Direct
Clathrin adaptor core protein	0.0002896	Direct
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.0009274	Direct
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.001461	Inherited
Class I aminoacyl-tRNA synthetases (RS), catalytic domain	0.002011	Inherited
Nitrogenase iron protein-like	0.002177	Inherited
BTB/POZ domain	0.03764	Inherited
CCCH zinc finger	0.05374	Inherited
Nucleosome core histones	0.08035	Inherited
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.2692	Inherited
G proteins	0.3046	Inherited
Protein kinases, catalytic subunit	0.8619	Inherited

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Skp1 dimerisation domain-like	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
GroEL equatorial domain-like	0.00000000007986	Direct
GroEL-intermediate domain like	0.00000000007986	Direct
GroEL apical domain-like	0.000000000384	Direct
Sm-like ribonucleoproteins	0.00000001169	Direct
Translation proteins SH3-like domain	0.0000001624	Direct
Nucleic acid-binding proteins	0.000003947	Direct
L30e-like	0.0000188	Direct
F1F0 ATP synthase subunit C	0.00002251	Direct
Ribosomal proteins S24e, L23 and L15e	0.00002251	Direct
S15/NS1 RNA-binding domain	0.00002251	Direct
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.00006285	Direct
Translational machinery components	0.00006376	Direct
"Winged helix" DNA-binding domain	0.0001418	Direct
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.0004564	Direct
Nucleotidylyl transferase	0.004702	Inherited
Histone-fold	0.02634	Inherited
POZ domain	0.02642	Inherited
CCCH zinc finger	0.02955	Inherited
Class II aaRS and biotin synthetases	0.2335	Inherited
Translation proteins	0.2335	Inherited
Ribosomal protein S5 domain 2-like	0.2952	Inherited
Protein kinase-like (PK-like)	0.7891	Inherited
SNARE-like	0.793	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
54695,81382 54695 - POZ domain 81382 - Skp1 dimerisation domain-like	0	Direct
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.00000000007986	Direct
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.00000000007986	Direct
81333,81333 81333 - F1F0 ATP synthase subunit C 81333 - F1F0 ATP synthase subunit C	0.000004803	Direct
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0.00002251	Direct
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	0.00005213	Direct
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.0001409	Direct
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.0004564	Direct
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.0004741	Direct
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	0.005993	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.03705	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.00000000007986	Direct
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.0004564	Direct

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

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Worm Phenotype (WP): meiotic progression during oogenesis variant

Superfamily

Family

Supra-domain (including individual superfamily)