Xenopus ANatomical entity (XAN): solid compound organ

Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype 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. Biomedical ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology
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 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 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
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 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 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 displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology
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
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
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.
UniProtKB KeyWords (KW) Ontology
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).
CTD Diseases (CD) Ontology
CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
CTD Chemicals (CC) Ontology
CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Succinyl-CoA synthetase domains	0	Direct
DnaJ/Hsp40 cysteine-rich domain	0	Direct
F1F0 ATP synthase subunit C	0	Direct
Moesin tail domain	0	Direct
Fibrinogen coiled-coil and central regions	0	Direct
Mib/herc2 domain-like	0	Direct
Subunits of heterodimeric actin filament capping protein Capz	0	Direct
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
FAS1 domain	0	Direct
Apolipoprotein A-I	0	Direct
Surp module (SWAP domain)	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
TK C-terminal domain-like	0	Direct
Annexin	0.001666	Inherited
Thioredoxin-like	0.001716	Inherited
UBC-like	0.00811	Inherited
Zn-binding ribosomal proteins	0.0106	Inherited
Actin depolymerizing proteins	0.01845	Inherited
LDH C-terminal domain-like	0.02605	Inherited
Translation proteins SH3-like domain	0.03173	Inherited
Spectrin repeat	0.08121	Inherited
p53-like transcription factors	0.808	Inherited
Homeodomain-like	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Ferritin	0	Direct
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	0	Direct
Mib/herc2 domain	0	Direct
FAS1 domain	0	Direct
HCDH C-domain-like	0	Direct
RUNT domain	0	Direct
F1F0 ATP synthase subunit C	0	Direct
NIPSNAP	0	Direct
Fibronectin type I module	0	Direct
Netrin-like domain (NTR/C345C module)	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Variant RING domain	0	Direct
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
Branched-chain alpha-keto acid dehydrogenase PP module	0	Direct
Moesin tail domain	0	Direct
CAT-like	0	Direct
Apolipoprotein A-I	0	Direct
Fibrinogen coiled-coil and central regions	0	Direct
Ribosomal protein L3	0	Direct
Phosphoribosylpyrophosphate synthetase-like	0	Direct
DJ-1/PfpI	0	Direct
Surp module (SWAP domain)	0	Direct
Serine carboxypeptidase-like	0	Direct
DnaJ/Hsp40 cysteine-rich domain	0	Direct
Succinyl-CoA synthetase domains	0	Direct
Proteasome subunits	0.00007295	Direct
Canonical RBD	0.0004546	Direct
Complement components	0.004245	Inherited
Glutathione peroxidase-like	0.01594	Inherited
LDH N-terminal domain-like	0.02514	Inherited
Linker histone H1/H5	0.02514	Inherited
Lactate & malate dehydrogenases, C-terminal domain	0.02514	Inherited
Spectrin repeat	0.06263	Inherited
Homeodomain	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
Mib/herc2 domain-like	0	Direct
DnaJ/Hsp40 cysteine-rich domain	0	Direct
Succinyl-CoA synthetase domains	0	Direct
Apolipoprotein A-I	0	Direct
F1F0 ATP synthase subunit C	0	Direct
Subunits of heterodimeric actin filament capping protein Capz	0	Direct
TK C-terminal domain-like	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
FAS1 domain	0	Direct
Surp module (SWAP domain)	0	Direct
Moesin tail domain	0	Direct
Fibrinogen coiled-coil and central regions	0	Direct
Annexin	0.001272	Inherited
Thioredoxin-like	0.001311	Inherited
UBC-like	0.006338	Inherited
Alpha-macroglobulin receptor domain	0.00832	Inherited
Zn-binding ribosomal proteins	0.00832	Inherited
Actin depolymerizing proteins	0.01459	Inherited
LDH C-terminal domain-like	0.02082	Inherited
Translation proteins SH3-like domain	0.02552	Inherited
Spectrin repeat	0.06786	Inherited
p53-like transcription factors	0.7765	Inherited
Homeodomain-like	1	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
82895,57424 82895 - TSP-1 type 1 repeat 57424 - LDL receptor-like module	0	Direct
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain	0	Direct
54631,54631 54631 - CBS-domain pair 54631 - CBS-domain pair	0	Direct
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains	0	Direct
54403,54403 54403 - Cystatin/monellin 54403 - Cystatin/monellin	0	Direct
48371,46785 48371 - ARM repeat 46785 - "Winged helix" DNA-binding domain	0	Direct
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	Direct
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24	0	Direct
57603,57440 57603 - FnI-like domain 57440 - Kringle-like	0	Direct
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	Direct
57938,49493 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain	0	Direct
46565,57938 46565 - Chaperone J-domain 57938 - DnaJ/Hsp40 cysteine-rich domain	0	Direct
57196,50494 57196 - EGF/Laminin 50494 - Trypsin-like serine proteases	0	Direct
52518,52922 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52922 - TK C-terminal domain-like	0	Direct
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.0004817	Direct
46966,47473 46966 - Spectrin repeat 47473 - EF-hand	0.0132	Inherited
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.01459	Inherited
47095,47095 47095 - HMG-box 47095 - HMG-box	0.02082	Inherited
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like	0.02082	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
51230,47005,52777 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	Direct
46565,57938,49493 46565 - Chaperone J-domain 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain	0	Direct
56436,56436,56436 56436 - C-type lectin-like 56436 - C-type lectin-like 56436 - C-type lectin-like	0	Direct
57196,49854,57535 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain 57535 - Complement control module/SCR domain	0	Direct
57938,49493,49493 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain 49493 - HSP40/DnaJ peptide-binding domain	0	Direct
53300,81995,81811 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	Direct
81995,81811,82754 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	Direct
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.005381	Inherited
46966,46966,47473 46966 - Spectrin repeat 46966 - Spectrin repeat 47473 - EF-hand	0.0132	Inherited