Plant ANatomical entity (PAN): fruit

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

Jump to [ Top · Hierarchy ]

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Skp1 dimerisation domain-like	0	Direct
RuBisCO, small subunit	0	Direct
beta-N-acetylhexosaminidase-like domain	0	Direct
beta-carbonic anhydrase, cab	0	Direct
Thiolase-like	0	Direct
Purple acid phosphatase, N-terminal domain	0.00000000000007905	Direct
Metallo-dependent phosphatases	0.00000000001049	Direct
POZ domain	0.0000000001496	Direct
MCP/YpsA-like	0.000000002422	Direct
Galactose-binding domain-like	0.00000005538	Direct
Magnesium transport protein CorA, transmembrane region	0.0000006697	Direct
(Trans)glycosidases	0.0000007392	Direct
Chlorophyll a-b binding protein	0.000001318	Direct
Acyl-CoA binding protein	0.000003394	Direct
Homodimeric domain of signal transducing histidine kinase	0.000004629	Direct
Transducin (alpha subunit), insertion domain	0.00001333	Direct
D-ribose-5-phosphate isomerase (RpiA), lid domain	0.00001333	Direct
Actin-like ATPase domain	0.00001655	Direct
GAF domain-like	0.00001876	Direct
Glycerol-3-phosphate (1)-acyltransferase	0.00002316	Direct
Trimeric LpxA-like enzymes	0.00005202	Direct
Seven-hairpin glycosidases	0.00006381	Direct
Cupredoxins	0.00009639	Direct
DNA-binding domain	0.0001249	Direct
Creatinase/aminopeptidase	0.0003492	Direct
HD-domain/PDEase-like	0.0004237	Direct
Homeodomain-like	0.0005262	Direct
Beta-D-glucan exohydrolase, C-terminal domain	0.0008114	Direct
Cytochrome P450	0.01276	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

Jump to [ Top · Hierarchy ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Phosphoenolpyruvate carboxylase	0	Direct
RuBisCO, small subunit	0	Direct
Skp1 dimerisation domain-like	0	Direct
glucose-1-phosphate thymidylyltransferase	0	Direct
MioX-like	0	Direct
Chalcone synthase-like	0	Direct
beta-N-acetylhexosaminidase catalytic domain	0	Direct
Receiver domain of the ethylene receptor	0	Direct
beta-carbonic anhydrase, cab	0	Direct
Purple acid phosphatase-like	0	Direct
Glycosyl hydrolases family 35 catalytic domain	0.00000000000003754	Direct
Purple acid phosphatase, N-terminal domain	0.0000000000002078	Direct
BTB/POZ domain	0.000000000008592	Direct
Homeodomain	0.0000000000985	Direct
MoCo carrier protein-like	0.0000000006523	Direct
GlmU C-terminal domain-like	0.000000001584	Direct
Hexokinase	0.00000003306	Direct
Glycosyl transferases group 1	0.0000001816	Direct
Multidomain cupredoxins	0.0000004563	Direct
Dihydrodipicolinate reductase-like	0.0000006899	Direct
Chlorophyll a-b binding protein	0.0000008284	Direct
Acyl-CoA binding protein	0.000003962	Direct
Magnesium transport protein CorA, transmembrane region	0.00001329	Direct
D-ribose-5-phosphate isomerase (RpiA), catalytic domain	0.00001436	Direct
D-ribose-5-phosphate isomerase (RpiA), lid domain	0.00001436	Direct
BAR domain	0.00001436	Direct
Transducin (alpha subunit), insertion domain	0.00001436	Direct
Class I alpha-1;2-mannosidase, catalytic domain	0.00006875	Direct
Homodimeric domain of signal transducing histidine kinase	0.00007564	Direct
GAF domain	0.0001402	Direct
GCC-box binding domain	0.0003923	Direct
Glycerophosphoryl diester phosphodiesterase	0.0004049	Direct
Creatinase/aminopeptidase	0.0004049	Direct
NagZ-like	0.000939	Direct
Beta-D-glucan exohydrolase, C-terminal domain	0.000939	Direct
Cytochrome P450	0.02426	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

Jump to [ Top · Hierarchy ]

Supra-domain (Single)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
beta-carbonic anhydrase, cab	0	Direct
beta-N-acetylhexosaminidase-like domain	0	Direct
Thiolase-like	0	Direct
Skp1 dimerisation domain-like	0	Direct
RuBisCO, small subunit	0	Direct
Purple acid phosphatase, N-terminal domain	0.00000000000006103	Direct
Metallo-dependent phosphatases	0.000000000008097	Direct
POZ domain	0.0000000001156	Direct
MCP/YpsA-like	0.000000001873	Direct
Galactose-binding domain-like	0.0000000429	Direct
Magnesium transport protein CorA, transmembrane region	0.00000052	Direct
(Trans)glycosidases	0.0000005739	Direct
Chlorophyll a-b binding protein	0.000001024	Direct
Acyl-CoA binding protein	0.00000264	Direct
Homodimeric domain of signal transducing histidine kinase	0.000003602	Direct
D-ribose-5-phosphate isomerase (RpiA), lid domain	0.00001039	Direct
Transducin (alpha subunit), insertion domain	0.00001039	Direct
Actin-like ATPase domain	0.00001291	Direct
GAF domain-like	0.00001464	Direct
Glycerol-3-phosphate (1)-acyltransferase	0.00001808	Direct
Trimeric LpxA-like enzymes	0.00004068	Direct
Seven-hairpin glycosidases	0.00004993	Direct
Cupredoxins	0.0000755	Direct
DNA-binding domain	0.00009793	Direct
Creatinase/aminopeptidase	0.0002749	Direct
HD-domain/PDEase-like	0.0003341	Direct
Homeodomain-like	0.0004154	Direct
Beta-D-glucan exohydrolase, C-terminal domain	0.000642	Direct
Cytochrome P450	0.01038	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

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

(show details)

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
55545,51445 55545 - beta-N-acetylhexosaminidase-like domain 51445 - (Trans)glycosidases	0	Direct
103657,50729 103657 - BAR/IMD domain-like 50729 - PH domain-like	0	Direct
55781,47384 55781 - GAF domain-like 47384 - Homodimeric domain of signal transducing histidine kinase	0	Direct
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like	3.181e-16	Direct
49363,56300 49363 - Purple acid phosphatase, N-terminal domain 56300 - Metallo-dependent phosphatases	0.00000000000006103	Direct
51445,49785 51445 - (Trans)glycosidases 49785 - Galactose-binding domain-like	0.0000000000007192	Direct
49785,49785 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like	0.00000000000539	Direct
53448,51161 53448 - Nucleotide-diphospho-sugar transferases 51161 - Trimeric LpxA-like enzymes	0.000000006784	Direct
49503,49503 49503 - Cupredoxins 49503 - Cupredoxins	0.0000001827	Direct
55961,55961 55961 - Bet v1-like 55961 - Bet v1-like	0.0000006544	Direct
51695,51695 51695 - PLC-like phosphodiesterases 51695 - PLC-like phosphodiesterases	0.000008881	Direct
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00001039	Direct
50729,57863 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger	0.00001039	Direct
57863,48403 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0.00001039	Direct
100950,75445 100950 - NagB/RpiA/CoA transferase-like 75445 - D-ribose-5-phosphate isomerase (RpiA), lid domain	0.00001039	Direct
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.00002347	Direct
47384,55874 47384 - Homodimeric domain of signal transducing histidine kinase 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0.0006294	Direct
51445,52279 51445 - (Trans)glycosidases 52279 - Beta-D-glucan exohydrolase, C-terminal domain	0.000642	Direct

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

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

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
55781,47384,55874 55781 - GAF domain-like 47384 - Homodimeric domain of signal transducing histidine kinase 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0	Direct
103657,50729,57863 103657 - BAR/IMD domain-like 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger	0	Direct
51445,49785,49785 51445 - (Trans)glycosidases 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like	0.0000000000002205	Direct
50729,57863,48403 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger 48403 - Ankyrin repeat	0.00001039	Direct