Xenopus ANatomical entity (XAN): anatomical entity in vitro

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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: XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)

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

+ 1: Xenopus anatomical entity [XAO:0000000] <9>

0: anatomical entity in vitro [XAO:0003007] <4> (28|33) (28|14|2)

- 1: cell-free extract [XAO:0004291] <1> (0|0) (0|0|0)

- 1: Keller explant [XAO:0003053] (0|0) (0|0|0)

- 1: activin-induced ectoderm [XAO:0003008] (0|0) (0|0|0)

- 1: disaggregated/reaggregated ectoderm treated with activin [XAO:0003009] (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)
KA1-like	0	Direct
4Fe-4S ferredoxins	0	Direct
Tim10-like	0	Direct
Mediator hinge subcomplex-like	0	Direct
Alpha-L RNA-binding motif	0	Direct
Subunits of heterodimeric actin filament capping protein Capz	0	Direct
PLP-binding barrel	0	Direct
Surp module (SWAP domain)	0	Direct
SPOC domain-like	0	Direct
Ferritin-like	0	Direct
Myosin phosphatase inhibitor 17kDa protein, CPI-17	0	Direct
Alanine racemase C-terminal domain-like	0	Direct
Nop domain	0	Direct
Ribosomal proteins L15p and L18e	0	Direct
LuxS/MPP-like metallohydrolase	0	Direct
Ribosomal proteins S24e, L23 and L15e	0	Direct
RNA-binding domain, RBD	0	Direct
UBC-like	0.00003053	Direct
Eukaryotic type KH-domain (KH-domain type I)	0.00003124	Direct
Cyclophilin-like	0.00004535	Direct
Sm-like ribonucleoproteins	0.00007074	Direct
Nucleic acid-binding proteins	0.00007493	Direct
Translation proteins SH3-like domain	0.00009267	Direct
ARM repeat	0.0004128	Direct
GroEL-intermediate domain like	0.00065	Direct
GroEL equatorial domain-like	0.00065	Direct
WD40 repeat-like	0.0009025	Direct
"Winged helix" DNA-binding domain	0.0009907	Direct

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Ferritin	0	Direct
Adenain-like	0	Direct
RuBisCo LSMT catalytic domain	0	Direct
Group II chaperonin (CCT, TRIC), intermediate domain	0	Direct
TRASH domain	0	Direct
MPP-like	0	Direct
Canonical RBD	0	Direct
Alanine racemase-like, N-terminal domain	0	Direct
Eukaryotic ODC-like	0	Direct
Tim10/DDP	0	Direct
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	Direct
Ribosomal proteins L15p and L18e	0	Direct
A20-like zinc finger	0	Direct
ECR1 N-terminal domain-like	0	Direct
Ran-binding domain	0	Direct
S-adenosylhomocystein hydrolase	0	Direct
Kinase associated domain 1, KA1	0	Direct
Nop domain	0	Direct
Surp module (SWAP domain)	0	Direct
Myosin phosphatase inhibitor 17kDa protein, CPI-17	0	Direct
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	Direct
B56-like	0	Direct
Cold shock DNA-binding domain-like	0.000002774	Direct
Ubiquitin-related	0.0000081	Direct
Tandem AAA-ATPase domain	0.00001563	Direct
UBC-related	0.00001734	Direct
Eukaryotic type KH-domain (KH-domain type I)	0.00002151	Direct
Cyclophilin (peptidylprolyl isomerase)	0.00003203	Direct
Sm motif of small nuclear ribonucleoproteins, SNRNP	0.00003203	Direct
TBP-associated factors, TAFs	0.0002031	Direct
Prefoldin	0.00048	Direct
Cyclin	0.0007307	Direct
Myb/SANT domain	0.0009903	Direct

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

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

Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
PLP-binding barrel	0	Direct
Surp module (SWAP domain)	0	Direct
LuxS/MPP-like metallohydrolase	0	Direct
Nop domain	0	Direct
Mediator hinge subcomplex-like	0	Direct
4Fe-4S ferredoxins	0	Direct
Alpha-L RNA-binding motif	0	Direct
SPOC domain-like	0	Direct
Myosin phosphatase inhibitor 17kDa protein, CPI-17	0	Direct
RNA-binding domain, RBD	0	Direct
Subunits of heterodimeric actin filament capping protein Capz	0	Direct
Ribosomal proteins L15p and L18e	0	Direct
KA1-like	0	Direct
Tim10-like	0	Direct
Ferritin-like	0	Direct
Ribosomal proteins S24e, L23 and L15e	0	Direct
Alanine racemase C-terminal domain-like	0	Direct
UBC-like	0.00002223	Direct
Eukaryotic type KH-domain (KH-domain type I)	0.00002276	Direct
Cyclophilin-like	0.00003316	Direct
Sm-like ribonucleoproteins	0.00005201	Direct
Nucleic acid-binding proteins	0.00005511	Direct
Translation proteins SH3-like domain	0.00006831	Direct
ARM repeat	0.0003098	Direct
GroEL-intermediate domain like	0.0004903	Direct
GroEL equatorial domain-like	0.0004903	Direct
WD40 repeat-like	0.0006839	Direct
"Winged helix" DNA-binding domain	0.0007513	Direct

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57196,100895 57196 - EGF/Laminin 100895 - Kazal-type serine protease inhibitors	0	Direct
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like	0	Direct
63411,63411 63411 - LuxS/MPP-like metallohydrolase 63411 - LuxS/MPP-like metallohydrolase	0	Direct
110324,50249 110324 - Ribosomal L27 protein-like 50249 - Nucleic acid-binding proteins	0	Direct
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	Direct
57756,57756 57756 - Retrovirus zinc finger-like domains 57756 - Retrovirus zinc finger-like domains	0	Direct
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0	Direct
64356,49447 64356 - SNARE-like 49447 - Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	Direct
52540,46785 52540 - P-loop containing nucleoside triphosphate hydrolases 46785 - "Winged helix" DNA-binding domain	0	Direct
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	Direct
48371,46785 48371 - ARM repeat 46785 - "Winged helix" DNA-binding domain	0	Direct
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.00000003089	Direct
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I)	0.000005084	Direct
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0005967	Direct

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
54791,54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I)	0	Direct
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0	Direct

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

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Xenopus ANatomical entity (XAN): anatomical entity in vitro

Superfamily

Family

Supra-domain (including individual superfamily)