Summary for ontology term: biopsy

Number of annotations with term: 32

Top positive-associated sequence

Taxonomy Sequence Recall
d__BacteriaCACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAAT0.100000
d__Bacteria;p__"Bacteroidetes";c__Flavobacteriia;o__"Flavobacteriales";f__Flavobacteriaceae;g__CloacibacteriumTACGGAGGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTCCGTAGGCGGACTTATAAGTCAGTGGTGAAAGCCTGTCGCTTAACGATAGAACTGCCATTGATACTGTAAGTCTTGAGTATATTTGAGGTAGCTGGAATAAGTAG0.066667
d__Bacteria;p__"Actinobacteria";c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae;g__CorynebacteriumTACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCCGGGGCTTAACTTCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGAGACTGGAATTCCTG0.066667
d__Bacteria;p__"Proteobacteria";c__Gammaproteobacteria;o__"Enterobacteriales";f__Enterobacteriaceae;g__Escherichia/ShigellaTACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGG0.066667
d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__RoseburiaTACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGAAGGCTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGGTCATCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAG0.066667
d__Bacteria;p__"Bacteroidetes";c__"Bacteroidia";o__"Bacteroidales";f__Bacteroidaceae;g__BacteroidesTACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACTGGTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGTCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGG0.066667
d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Clostridium XlVaTACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCGAAGCAAGTCTGAAGTGAAAACCCAGGGCTCAACCCTGGGACTGCTTTGGAAACTGTTTTGCTAGAGTGTCGGAGAGGTAAGTGGAATTCCTAG0.066667
d__Bacteria;p__"Proteobacteria";c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__PseudomonasTACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTG0.033333
d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__StaphylococcusTACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGGAGAGGAAAGTGGAATTCCATG0.033333
d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__PeptostreptococcusTACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGTGGTCTTTCAAGTCGGTGGTTAAAGGCTACGGCTCAACCGTAGTTAGCCTCCGAAACTGGAAGACTTGAGTGCAGGAGAGGAAAGTGGAATTCCCAGT0.033333

Top negative-associated sequence

Taxonomy Sequence Recall
d__Bacteria;p__Firmicutes;c__Bacilli;o__LactobacillalesTACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATG0.500000
d__Bacteria;p__"Actinobacteria";c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__ActinomycesTACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGCTGGTCGCGTCTGTCGTGAAATCCTCTGGCTTAACTGGGGGCTTGCGGTGGGTACGGGCCGGCTTGAGTGCGGTAGGGGAGACTGGAACTCCTGG0.500000
d__Bacteria;p__"Actinobacteria";c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__ActinomycesTACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATTCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGG0.500000
d__Bacteria;p__"Actinobacteria";c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__ActinomycesTACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGG0.500000
d__Bacteria;p__FirmicutesTACGTAGATGGCGAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGTGTAGGCGGGATCATAAGTTGCGTGTGAAATGCAGGGGCTCAACCCCTGAACTGCGCGCAAAACTGTGGTTCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCGG0.500000
d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_Incertae Sedis XI;g__ParvimonasTACGTATGGGGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGTACGTAGGCGGTCTATTAAGTCAGGTGTGAAAGCGTGAGGCTTAACCTCATTAAGCACTTGAAACTGATAGACTTGAGTGAAGGAGAGGAAAGTGGAATTCCTAGT0.500000
d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptoniphilaceae;g__PeptoniphilusTACGTAGGGGGCTAGCGTTGTCCGGAATCACTGGGCGTAAAGGGTTCGCAGGCGGCAATGCAAGTCAGATGTAAAAGGCAAAGGCTCAACCTTTGTAAGCATCTGAAACTGTATAGCTTGAGAAGTGTAGAGGCAAGTGGAATTTTTAGT0.500000
d__Bacteria;p__"Bacteroidetes";c__"Bacteroidia";o__"Bacteroidales";f__"Porphyromonadaceae";g__PorphyromonasTACGGAGGATACGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGTGGTCCTGCAAGTCAGTGGTGAAAAGCTGAGGCTCAACCTCAGCCTTGCCGTTGAAACTGCAAGACTTGAGAGTACATGATGTGGGCGGAATGCGTAG0.500000
d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__StreptococcusTACGTAGGTCCCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGT0.500000
d__Bacteria;p__"Bacteroidetes";c__"Bacteroidia";o__"Bacteroidales";f__"Prevotellaceae";g__PrevotellaTACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCTGTCTATTAAGCGTGTTGTGAAATTTACCGGCTCAACCGGTGGCTTGCAGCGCGAACTGGTCGACTTGAGTATGCAGGAAGTAGGCGGAATTCATGG0.500000

Top COMMON/DOMINANT/HIGH sequence

Taxonomy Sequence F-Score
d__BacteriaTGATAAACCTTTAGCAATAAACCAAAGTTTAACTAAGCCATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAACCGGCATAAAGAGTGTTTTAGATCAATTCCCCTCAATAAA0.173913
d__Bacteria;p__"Bacteroidetes";c__"Bacteroidia";o__"Bacteroidales";f__Bacteroidaceae;g__BacteroidesTACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGG0.166667
d__BacteriaTGATAAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCTAGGGTTCGTCAAGTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAACCGGCGTAAAGAGTGTTTTAGATCAATTCCCCTCAATAAA0.166667
d__BacteriaTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAA0.163934
d__BacteriaCACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAAT0.160714
d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__WeissellaTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGTGTGATGAAGGGTTTCGGCTCGTAAAACACTGTTGTAAGAGAAGAATGACATTGAGAGTAACTGTTCAATGTGTGACGGTATCTTACCAGAAAGGAACGGC0.153846
d__Bacteria;p__"Proteobacteria";c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__HelicobacterTAGGGAATATTGCTCAATGGGGGAAACCCTGAAGCAGCAACGCCGCGTGGAGGATGAAGGTTTTAGGATTGTAAACTCCTTTTGTTAGAGAAGATAATGACGGTATCTAACGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTA0.150000
d__BacteriaAACTAACGATCGCCTACTGGGGAGCAGAGTTTCTACCCAGAAGAGGAAACACAGCTGCTATATACAGTTGCGCAGGGCGTGCACTGCACAAGGGCCCCTCCCATCTCTTTTCATACTGCAGATTTGTATGTTGTGAATGAAATTGTCCAG0.146341
d__BacteriaTGATAAACCTTTAGCAATAAACGAAAGTTTAACTGAGCTATACTAACTTTAGGGTTGGTTAATTTCATGCCAGCCACCACGGTCATACGATGAACCCAAGCTAATAGAGACTGGCGTAAAGAATGTTTTACATTATCCCTCAATAAAGCT0.137931
d__Bacteria;p__FirmicutesTACGTATGGGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGTGCGTAGGTGGTGGCTTAAGCGCAGGGTTTAAGGCAATGGCTTAACTATTGTTCGCCTTGCGAACTGGGTCACTTGAGTACAGGAGAGGAAAGCGGAATTCCTAGT0.127660

Annotations:

common ontology terms
term enrichment score
TermScore
biopsy0.890351
biopsy site0.527027
rectum0.315789
colon0.292683
sigmoid colon0.272727
terminal ileum0.272727
mucosa of stomach0.238095
ulcerative colitis0.233333
children0.200000
intestinal mucosa0.175439
LOWER IN biopsy site0.166667
LOWER IN biopsy0.150000
helicobacter pylori infectious disease0.146341
left colon0.136364
LOWER IN ulcerative colitis0.136364
right colon0.127660
south korea0.108696
stomach0.085470
human adult stage0.070423
crohn's disease0.060606
LOWER IN crohn's disease0.060606
LOWER IN luminal content0.058824
luminal content0.058824
severe0.058824
LOWER IN mild0.058824
mild0.058824
LOWER IN severe0.058824
helicobacter pylori0.058824
LOWER IN left colon0.055556
LOWER IN right colon0.054054
homo sapiens0.050360
LOWER IN rectum0.046512
caecum0.045455
child0.045455
germany0.044444
pathogen0.044444
united states of america0.031571
adult0.022209
control0.019900
feces0.017341
LOWER IN feces0.017341
china0.011211
LOWER IN control0.009217
Fraction of dbbact annotations with this term covered by the query
TermScore
crohn's disease1.000000
LOWER IN crohn's disease1.000000
biopsy0.875000
LOWER IN biopsy site0.750000
biopsy site0.750000
colon0.666667
sigmoid colon0.500000
terminal ileum0.500000
children0.500000
LOWER IN luminal content0.500000
luminal content0.500000
severe0.500000
LOWER IN mild0.500000
mild0.500000
LOWER IN severe0.500000
mucosa of stomach0.500000
helicobacter pylori0.500000
LOWER IN biopsy0.375000
helicobacter pylori infectious disease0.333333
rectum0.272727
left colon0.250000
LOWER IN left colon0.250000
ulcerative colitis0.250000
LOWER IN ulcerative colitis0.250000
LOWER IN right colon0.200000
right colon0.200000
intestinal mucosa0.200000
LOWER IN rectum0.090909
south korea0.083333
pathogen0.076923
stomach0.058824
human adult stage0.045455
germany0.034483
caecum0.027778
child0.027778
homo sapiens0.025830
united states of america0.016194
adult0.011561
control0.010811
feces0.009554
LOWER IN feces0.009554
china0.005814
LOWER IN control0.005405
Fraction of annotations for the query sequences containing the term
TermScore
homo sapiens1.000000
biopsy0.906250
united states of america0.625000
biopsy site0.406250
rectum0.375000
adult0.281250
ulcerative colitis0.218750
sigmoid colon0.187500
terminal ileum0.187500
colon0.187500
intestinal mucosa0.156250
china0.156250
human adult stage0.156250
stomach0.156250
mucosa of stomach0.156250
south korea0.156250
caecum0.125000
children0.125000
control0.125000
child0.125000
feces0.093750
LOWER IN biopsy site0.093750
LOWER IN biopsy0.093750
LOWER IN feces0.093750
left colon0.093750
right colon0.093750
LOWER IN ulcerative colitis0.093750
helicobacter pylori infectious disease0.093750
germany0.062500
crohn's disease0.031250
LOWER IN control0.031250
LOWER IN crohn's disease0.031250
LOWER IN luminal content0.031250
luminal content0.031250
LOWER IN right colon0.031250
LOWER IN left colon0.031250
LOWER IN rectum0.031250
severe0.031250
LOWER IN mild0.031250
mild0.031250
LOWER IN severe0.031250
pathogen0.031250
helicobacter pylori0.031250
Exp. ID User ID Description Date Region Flag Sequences
409amnon high in right colon compared to left colon in homo sapiens united states of america colon biopsy site biopsy 2018-11-22v4No1 / 1
569amnonHelicobacter pylori pathogen (other homo sapiens, stomach, pathogen, biopsy, south korea, mucosa of stomach, helicobacter pylori infectious disease, helicobacter pylori)2019-12-16v3No1 / 1
410amnonhigher in biopsies of severe treatment naive ulcerative colitis patients compared to mild ( high in severe ulcerative colitis compared to mild in homo sapiens united states of america rectum biopsy site child biopsy )2018-11-22v4No1 / 5
569amnonhigh freq. in gastric biopsies of patients positive for h. pylori (dominant homo sapiens, stomach, biopsy, south korea, mucosa of stomach, helicobacter pylori infectious disease)2019-12-16v3No1 / 5
856amnon high in control compared to ulcerative colitis ulcerative colitis in homo sapiens rectum adult biopsy intestinal mucosa china human adult stage 2022-01-09v3No1 / 6
569amnonhigh freq. in gastric biopsies of patients negative for h. pylori (dominant homo sapiens, stomach, biopsy, south korea, mucosa of stomach)2019-12-16v3No1 / 9
51amnonlower in stool compared to biopsies ( high in biopsy site biopsy compared to feces in homo sapiens united states of america )2017-01-19v4No1 / 14
409amnon high in left colon compared to right colon in homo sapiens united states of america colon biopsy site biopsy 2018-11-22v4No1 / 15
409amnondominant homo sapiens, united states of america, left colon, biopsy site, adult, biopsy2018-11-22v4No1 / 15
19amnonhigh freq in biopsies of children (IBD study) (dominant homo sapiens, united states of america, rectum, caecum, colon, sigmoid colon, terminal ileum, biopsy, children)2016-11-14v4No1 / 16
51amnondominant homo sapiens, united states of america, biopsy site, biopsy2017-01-19v4No1 / 16
409amnondominant homo sapiens, united states of america, right colon, biopsy site, adult, biopsy2018-11-22v4No1 / 20
856amnondominant homo sapiens, control, rectum, adult, biopsy, intestinal mucosa, china, human adult stage2022-01-09v3No1 / 23
714amnondominant homo sapiens, sigmoid colon, terminal ileum, biopsy, germany2028-05-21v3No1 / 25
856amnondominant homo sapiens, rectum, ulcerative colitis, adult, biopsy, intestinal mucosa, ulcerative colitis, china, human adult stage2022-01-09v3No1 / 25
410amnonlower in biopsies of severe treatment naive ulcerative colitis patients compared to mild ( high in mild compared to severe ulcerative colitis in homo sapiens united states of america rectum biopsy site child biopsy )2018-11-22v4No1 / 26
856amnoncommon homo sapiens, rectum, ulcerative colitis, adult, biopsy, intestinal mucosa, ulcerative colitis, china, human adult stage2022-01-09v3No1 / 33
19amnonhigher in CD compared to control in biopsies ( high in crohn's disease compared to control in homo sapiens united states of america rectum caecum colon sigmoid colon terminal ileum biopsy children )2016-11-14v4No1 / 34
51amnoncommon homo sapiens, united states of america, biopsy site, biopsy2017-01-19v4No1 / 36
51amnonhigher in stool compared to biopsies ( high in feces compared to biopsy site biopsy in homo sapiens united states of america )2017-01-19v4No1 / 37
409amnonhigher in colon biopsies compared to stool and luminal content ( high in biopsy site biopsy compared to feces luminal content in homo sapiens united states of america )2018-11-22v4No1 / 38
714amnoncommon homo sapiens, sigmoid colon, terminal ileum, biopsy, germany2028-05-21v3No1 / 40
19amnoncommon in biopsies of children (IBD study) (common homo sapiens, united states of america, rectum, caecum, colon, sigmoid colon, terminal ileum, biopsy, children)2016-11-14v4No1 / 40
409amnonlower in colon biopsies compared to stool and luminal content ( high in feces luminal content compared to biopsy site biopsy in homo sapiens united states of america )2018-11-22v4No1 / 42
856amnoncommon homo sapiens, control, rectum, adult, biopsy, intestinal mucosa, china, human adult stage2022-01-09v3No1 / 48
569amnoncommon in gastric biopsies of patients positive for h. pylori (common homo sapiens, stomach, biopsy, mucosa of stomach, helicobacter pylori infectious disease, south korea)2019-12-16v3No1 / 77
569amnoncommon in gastric biopsies of patients negative for h. pylori (common homo sapiens, stomach, biopsy, south korea, mucosa of stomach)2019-12-16v3No1 / 85
409amnoncommon homo sapiens, united states of america, right colon, biopsy site, adult, biopsy2018-11-22v4No1 / 97
409amnoncommon homo sapiens, united states of america, left colon, biopsy site, adult, biopsy2018-11-22v4No1 / 118
410amnonlower in feces compared to rectal biopsies in children with treatment naive uc ( high in rectum biopsy site biopsy compared to feces in homo sapiens united states of america child ulcerative colitis )2018-11-22v4No1 / 118
410amnonhigher in feces compared to rectal biopsies in children with treatment naive uc ( high in feces compared to rectum biopsy site biopsy in homo sapiens united states of america child ulcerative colitis )2018-11-22v4No1 / 126
19amnonhigher in controls compared to CD in biopsies ( high in control compared to crohn's disease in homo sapiens united states of america rectum caecum colon sigmoid colon terminal ileum biopsy children )2016-11-14v4No1 / 459

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