Plant structure DEvelopment stage (PDE): seed development stage

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)
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
NAD(P)-binding Rossmann-fold domains	0.000000000005166	Direct
GroEL-intermediate domain like	0.000000002576	Direct
GroEL equatorial domain-like	0.000000004758	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.00000002182	Direct
Heat shock protein 70kD (HSP70), peptide-binding domain	0.00000002296	Direct
GroEL apical domain-like	0.00000002354	Direct
14-3-3 protein	0.0000001059	Direct
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0.000000448	Direct
Actin-like ATPase domain	0.0000006309	Direct
S-adenosylmethionine synthetase	0.000002532	Direct
Heat shock protein 70kD (HSP70), C-terminal subdomain	0.000005751	Direct
TK C-terminal domain-like	0.00001712	Direct
LDH C-terminal domain-like	0.00001712	Direct
Succinyl-CoA synthetase domains	0.00003602	Direct
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0.00003736	Direct
Citrate synthase	0.00008178	Direct
RmlC-like cupins	0.0001454	Direct
Apolipoprotein A-I	0.0001592	Direct
Ferritin-like	0.0001782	Direct
Aldolase	0.0002513	Direct
Mannose-binding lectins	0.0002522	Direct
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.0003474	Direct
GST C-terminal domain-like	0.0005655	Direct
Trimeric LpxA-like enzymes	0.0006184	Direct
Thiamin diphosphate-binding fold (THDP-binding)	0.0008019	Direct
Single hybrid motif	0.0008019	Direct

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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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
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Proteasome subunits	0.000000000006435	Direct
Heat shock protein 70kD (HSP70), peptide-binding domain	0.00000003993	Direct
14-3-3 protein	0.0000003016	Direct
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0.000001078	Direct
CoA-binding domain	0.000004347	Direct
S-adenosylmethionine synthetase	0.000004347	Direct
Actin/HSP70	0.000006498	Direct
FAD/NAD-linked reductases, N-terminal and central domains	0.00001253	Direct
Heat shock protein 70kD (HSP70), C-terminal subdomain	0.00001354	Direct
GroEL-like chaperone, apical domain	0.00001768	Direct
GroEL-like chaperone, intermediate domain	0.00001768	Direct
Group II chaperonin (CCT, TRIC), ATPase domain	0.00001768	Direct
GroEL chaperone, ATPase domain	0.00001768	Direct
Group II chaperonin (CCT, TRIC), intermediate domain	0.00002106	Direct
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	0.00003103	Direct
Lactate & malate dehydrogenases, C-terminal domain	0.00003426	Direct
LDH N-terminal domain-like	0.00003426	Direct
Germin/Seed storage 7S protein	0.00004237	Direct
Succinyl-CoA synthetase domains	0.00006124	Direct
PDI-like	0.0001011	Direct
GAPDH-like	0.0001386	Direct
Citrate synthase	0.0001386	Direct
Group II chaperonin (CCT, TRIC), apical domain	0.0001592	Direct
Class I aldolase	0.0001592	Direct
RecA protein-like (ATPase-domain)	0.00024	Direct
Pathogenesis-related protein 10 (PR10)-like	0.0002687	Direct
Formate/glycerate dehydrogenases, substrate-binding domain	0.0002687	Direct
CAT-like	0.0002687	Direct
Tyrosine-dependent oxidoreductases	0.0003589	Direct
Mannose-binding lectins	0.0004912	Direct
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.0006746	Direct
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	0.000758	Direct

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)
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
NAD(P)-binding Rossmann-fold domains	0.000000000004342	Direct
GroEL-intermediate domain like	0.000000002165	Direct
GroEL equatorial domain-like	0.000000004	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.00000001835	Direct
Heat shock protein 70kD (HSP70), peptide-binding domain	0.0000000193	Direct
GroEL apical domain-like	0.0000000198	Direct
14-3-3 protein	0.0000000891	Direct
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0.0000003769	Direct
Actin-like ATPase domain	0.0000005308	Direct
S-adenosylmethionine synthetase	0.000002131	Direct
Heat shock protein 70kD (HSP70), C-terminal subdomain	0.000004841	Direct
TK C-terminal domain-like	0.00001442	Direct
LDH C-terminal domain-like	0.00001442	Direct
Succinyl-CoA synthetase domains	0.00003034	Direct
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0.00003147	Direct
Citrate synthase	0.00006893	Direct
RmlC-like cupins	0.0001227	Direct
Apolipoprotein A-I	0.0001343	Direct
Ferritin-like	0.0001504	Direct
Aldolase	0.0002122	Direct
Mannose-binding lectins	0.000213	Direct
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.0002937	Direct
GST C-terminal domain-like	0.0004782	Direct
Trimeric LpxA-like enzymes	0.0005232	Direct
Single hybrid motif	0.0006791	Direct
Thiamin diphosphate-binding fold (THDP-binding)	0.0006791	Direct
Formate/glycerate dehydrogenase catalytic domain-like	0.0008542	Direct

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)
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	0.000000002165	Direct
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.000000002165	Direct
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0.0000000193	Direct
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.0000001242	Direct
51905,55424 51905 - FAD/NAD(P)-binding domain 55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0.0000003769	Direct
100920,100934 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain 100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain	0.000001572	Direct
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0.000002131	Direct
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like	0.00001442	Direct
51101,51101 51101 - Mannose-binding lectins 51101 - Mannose-binding lectins	0.00001442	Direct
52518,52922 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52922 - TK C-terminal domain-like	0.00001442	Direct
51735,55347 51735 - NAD(P)-binding Rossmann-fold domains 55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	0.00003147	Direct
52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like	0.0001504	Direct
52283,51735 52283 - Formate/glycerate dehydrogenase catalytic domain-like 51735 - NAD(P)-binding Rossmann-fold domains	0.0005846	Direct
52833,47616 52833 - Thioredoxin-like 47616 - GST C-terminal domain-like	0.0009819	Direct

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)
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.000000002165	Direct
53067,53067,100920 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0.0000000193	Direct
51101,51101,51101 51101 - Mannose-binding lectins 51101 - Mannose-binding lectins 51101 - Mannose-binding lectins	0.000001301	Direct
53067,100920,100934 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain 100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain	0.000001572	Direct
55973,55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase	0.000002131	Direct
52833,52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like 52833 - Thioredoxin-like	0.0003821	Direct