The Jackson Lab
Cell Type ontology mappings to Revision 1.23
$version 0.7$
The Arabidopsis Information Resource (TAIR)
National Cancer Institute Thesaurus mappings to version December 2007 (07.12e)
James Malone
Helen Parkinson
classified
Drosophila Gross Anatomy ontology Revision 1.22 December 11 2007
Zebrafish Anatomy and Development ontology mappings version 1.14 October 24 2007
CRISP Thesaurus Version 2.5.2.0
Disease Ontology mappings to DiseaseOntology3 revision 2
MAT version 3.0
hermaphrodite gonad
MAT:0000165
amnioserosa anlage in statu nascendi
FBbt:00005422
sigmoid colon
MAT:0000314
Leiomyosarcoma
DOID:1967
adenoma
James Malone
A neoplasm arising from the epithelium. It may be encapsulated or non-encapsulated but non-invasive. The neoplastic epithelial cells may or may not display cellular atypia or dysplasia. In the gastrointestinal tract, when dysplasia becomes severe it is sometimes called carcinoma in situ. Representative examples are pituitary gland adenoma, follicular adenoma of the thyroid gland, and adenomas (or adenomatous polyps) of the gastrointestinal tract.
NCI Thesaurus: C2855
genetic factor
plant egg
MAT:0000213
gastrula 50%-epiboly
ZFS:0000017
malignant peripheral nerve sheath tumor class
DOID:5940
wing
MAT:0000202
plant component
MAT:0000003
plant reproductive system
MAT:0000514
mixed sex population
The total number of individuals inhabiting a particular region or area.
astrocytic tumor
DOID:3069
MOLT-4
jejunum
MAT:0000045
Wilms' tumor
nephroblastoma
DOID:2414
meningitis
DOID:9471
multipotent stem cell
multipotent adult progenitor cell
CL:0000048
animal body part
MAT:0000293
genetic disorder
James Malone
Genetic Diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders.
NCI Metathesaurus http://ncimeta.nci.nih.gov/MetaServlet/ResultServlet?cui=C0019247 Date Accessed: 30th October 2007
male reproductive system
male genital system
MAT:0000029
leukemia
DOID:1240
descending colon
MAT:0000313
adenoid cystic carcinoma
DOID:4866
metabolic syndrome
haltere
balancer organ
FBbt:00004783
MAT:0000203
gastrula 75%-epiboly
ZFS:0000020
amygdala
amygdala central nucleus
NCI Thesaurus: C12440
MAT:0000289
fungal component
MAT:0000002
adult
MAT:0000403
plant developmental tissue
MAT:0000518
astrocytoma
DOID:3069
mesangial phagocyte
mesangial cell
CL:0000777
129S1/SvImJ
James Malone
http://jaxmice.jax.org/strain/002248.html
unspecified peripheral T-cell lymphoma
integumental system
MAT:0000033
mouse strain
James Malone
Strain or line specific to mouse
generation
The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture; otherwise the number of generations.
adipose tissue
NCI Thesaurus: C12472
pericardium
MAT:0000454
rectum
MAT:0000050
animal ovary
MAT:0000125
labelling
The process of marking a material in some way for experimental purposes. E.g. the labelling of a nucleic acid with biotin in a microarray experiment
amyotrophic lateral sclerosis
DOID:332
gastrula 90%-epiboly
ZFS:0000021
metastatic prostate cancer
blastula 128-cell
ZFS:0000008
liver
MAT:0000097
skeleton
skeletal system
MAT:0000032
behavioural disease
behavioral disease
James Malone
A bacterial disease is a disease factor that is caused primarily by bacteria.
DOID:150
midbrain
MAT:0000106
megakaryocyte
CL:0000556
atmosphere
James Malone
The atmospheric conditions used to culture or grow an organism.
NIH3T3
abdominal skin
NCI Thesaurus: C52758
adenosquamous lung carcinoma
DOID:4829
gene knock out
mucoid ductal carcinoma
large cell neuroendocrine carcinoma
DOID:5721
anal region
anus
MAT:0000042
267B1
unfertilized egg
unfertilised egg
female gamete
MAT:0000124
anal pad specific anlage
FBbt:00005482
gastrula bud
ZFS:0000022
skeletal muscle
MAT:0000302
blastula 1k-cell
ZFS:0000011
thymus
MAT:0000080
atopic eczema
DOID:2771
sensory system
MAT:0000031
muscle cell
CL:0000187
ileum
MAT:0000282
epithalamus
MAT:0000422
celiac disease
DOID:10608
NCI-H929
abdominal cavity
NCI Thesaurus: C12664
megakaryocyte progenitor cell
CL:0000553
digit
MAT:0000285
lymphoblastic leukemia MOLT-4
gastrula germ-ring
ZFS:0000018
pollen tube
MAT:0000217
CS57732
James Malone
CS57732 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158756&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158756&type=germplasm
syndrome
James Malone
A set of symptoms or conditions that occur together and suggest the presence of a certain disease or an increased chance of developing the disease.
NCI Metathesaurus http://ncimeta.nci.nih.gov/MetaServlet/ResultServlet?cui=C0039082 Date accessed: 30th October 2007
267B1 Ki-ras
keratinocyte
CL:0000312
gastrointestinal stromal tumor
DOID:9253
adipose tissue brown MMHCC
brown fat
bulbus arteriosus
NCI Thesaurus: C22704
sjogren syndrome
DOID:12894
sporadic amyotrophic lateral sclerosis
Sporadic amyotrophic lateral sclerosis is a amyotrophic lateral sclerosis in which there is no known cause, such as no family history.
_temp bin organism part
temp holding class to be placed as hierarchy is restructured
CS57620
James Malone
CS57620 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158644&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158644&type=germplasm
BDC2.5/NOD
James Malone
BDC2.5/NOD is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/004460.html
JAX:004460
mesothelioma
DOID:2645
continuant
An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
A heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
colon
MAP:0000001
NCI Thesaurus: C12382
respiratory system
MAT:0000030
thyroid
MAT:0000081
electrical current
Formerly class "current milliamperes"
James Malone
The movement of electrical charges in a conductor measured in milliamperes.
atrial fibrillation
DOID:11276
DEL cells
ZFA:0000711
pollen
MAT:0000216
ploidy
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
haploid, diploid, triploid
MALT lymphoma
gastrula stage
MAT:0000063
CS57731
James Malone
CS57731 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158755&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158755&type=germplasm
systemic scleroderma
systemic sclerosis
DOID:418
forelimb
upper limb
MAT:0000394
gastric intestinal type adenocarcinoma
DOID:8026
293T
adipose tissue MMHCC
NCI Thesaurus: C22703
knock in expression
Replacement of a gene by an altered version of the same gene using homologous recombination resulting in a gain of function.
familial amyotrophic lateral sclerosis
Familial amyotrophic lateral sclerosis is a amyotrophic lateral sclerosis in which a family history of the disease exists.
CS57621
James Malone
CS57621 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158645&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158645&type=germplasm
small intestine
MAT:0000047
metabolism disease
DOID:0014667
endocardium
MAT:0000455
CBA/CaJ
James Malone
CBA/CaJ is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000654.html
JAX:000654
parathyroid
MAT:0000082
cutaneous melanoma
cancer of skin
skin melanoma
DOID:8923
renal system
MAT:0000027
DP thymocyte
nontransformed thymocyte
thymocyte
CL:0000809
cololrectal tumor
atrioventricular node
NCI Thesaurus: C32161
MAT:0000498
temperature
The temperature that a biosource is exposed to.
animal component
MAT:0000001
MELAS syndrome
DOID:3687
hindlimb
lower limb
MAT:0000395
microspore
MAT:0000215
type I diabetes mellitus
diabetes mellitus type 1
DOID:9744
inflorescence
MAT:0000233
transverse colon
MAT:0000312
gastric adenocarcinoma
DOID:3717
293TsiLL
gastrula shield
ZFS:0000019
CB6F1
James Malone
CB6F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100007.html
JAX:100007
adrenal gland
MAT:0000071
NCI Thesaurus: C12666
mesenchymal stem cell
conditioned mesenchymal stem cell
NCI Thesaurus: C43423
T lymphocyte
T lymphoma cell
CL:0000542
colon carcinoma
DOID:1520
CS57622
James Malone
CS57622 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158646&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158646&type=germplasm
nervous system
MAT:0000026
atrium
MAT:0000496
FBbt:00005615
Daudi Burkitt's lymphoma
hatching gland
MAT:0000180
CS57733
James Malone
CS57733 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158757&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158757&type=germplasm
anatomy basic component
MAT:0000000
invertebrate limb
invertebrata limb
MAT:0000095
megaspore
MAT:0000214
MMHCC part
An MMHCC (Mouse Models of Human Cancers Consortium) part is an organism part that has been modelled by the MMHCC, a program to develop and refine experimental models that reflect the etiology and progression of human cancer.
NCI Thesaurus: C19750
ascending colon
MAT:0000311
post-traumatic stress disorder
traumatic neurosis
posttraumatic stress disorder
James Malone
DOID:2055
NCI Thesaurus: C3389
3T3-L1
hatching stage
ZFS:0000033
TBP-71Q-16
James Malone
TBP-71Q-16 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/008216.html
JAX:008216
adrenal cortex
MAT:0000494
NCI Thesaurus: C12396
temporal factor
amnioserosa
FBbt:00000095
ganglioneuroblastoma
DOID:4163
colon adenocarcinoma
DOID:234
mesodermal cell
CL:0000222
muscle system
muscular system
MAT:0000025
Ewing family tumor
DOID:3369
neurohemal organ
neurohaemal organ
FBbt:00001717
MAT:0000212
autoimmune pancreatitis
DOID:4989
mating type alpha
MO_637
azoospermia
DOID:14227
rhizome
MAT:0000219
frontal lobe
MAT:0000505
cardiac mesoderm primordium
FBbt:00005541
Crohn's disease
DOID:4039
pharyngula prim-15
ZFS:0000030
sap
MAT:0000350
paired fin skeleton
MAT:0000278
ductal breast carcinoma
DOID:3008
cervix
MAT:0000292
follicular thyroid carcinoma
follicular carcinoma
DOID:3962
endometriosis
DOID:289
colorectal adenocarcinoma
colorectal cancer
DOID:9256
CS57615
James Malone
CS57615 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158639&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158639&type=germplasm
MCF 10A
Lewis
James Malone
RGD:737932
circular visceral muscle fibers
FBbt:00005072
embryonic dorsal apodeme
FBbt:00005745
R43
tepal
MAT:0000356
600MPE
CS57655
James Malone
CS57655 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158679&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158679&type=germplasm
anterior endoderm anlage
FBbt:00000210
platelet
CL:0000233
psoriasis
DOID:8893
pineal gland
MAT:0000448
meristem
Meristem is a plant component consisting of undifferentiated plant issue - the botanical equivalent of animal stem cells.
MAT:0000006
experimental autoimmune encephalomyelitis
DOID:3046
plasmacytoid dendritic cell
CL:0000784
telencephalon
MAT:0000421
pharyngula prim-25
ZFS:0000031
crystal cell
FBbt:00001690
median fin skeleton
MAT:0000277
colon mucinous adenocarcinoma
DOID:3029
bulb
MAT:0000367
R28
vulva
MAT:0000169
CS57616
James Malone
CS57616 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158640&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158640&type=germplasm
ductal carcinoma in situ
carcinoma in situ of breast
DOID:8791
ganglioneuroma
NCI Thesaurus:C3049
embryonic dorsal epidermis
FBbt:00005744
circular visceral mesoderm primordium
FBbt:00000107
Sprague Dawley
James Malone
RGD:70508
CS57658
James Malone
CS57658 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158682&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158682&type=germplasm
fruit
MAT:0000232
A549
cardiac atrium
atrial chamber
NCI Thesaurus: C12728
protocol factor
Possibly import of protocol application from OBI 1.0
James Malone
A protocol factor is an experimental factor which describes factors that describe the protocol design of an experiment.
seed
MAT:0000008
thymus
MAT:0000080
phyllid
MAT:0000276
diencephalon
MAT:0000420
pharyngula prim-5
ZFS:0000029
crystal cell specific anlage
FBbt:00005463
GM12873
parasitic Infection
NCI Thesaurus: C27864
DOID:1398
pterygium
DOID:10526
CS57618
James Malone
CS57618 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158642&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158642&type=germplasm
large intestine
hindgut
MAT:0000046
common variable immunodeficiency
CVID
DOID:12177
apoplasm
MAT:0000348
AU565
sensillum
MAT:0000163
CS57660
James Malone
CS57660 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158684&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158684&type=germplasm
dermis
MAT:0000153
MCF12A
petal
MAT:0000354
classifier prediction
An extrapolation into the future of data into a class with specified label.
infant
juvenile stage
MIAA:0000402
thallus
MAT:0000248
shoot
MAT:0000009
GM12155
meninges
MAT:0000113
plexiform neurofibroma
DOID:5151
carcinoma
James Malone
A type of malignant cancer that arises from epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases.
GM12874
thalamus
MAT:0000109
segmentation stage
cultivar
James Malone
A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.
malaria
DOID:12365
CS57619
James Malone
CS57619 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158643&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158643&type=germplasm
ductal adenocarcinoma
DOID:3008
connective tissue
tendon
fascia
MAT:0000301
columnar neuron
intermediolateral column motoneuron
CL:0000112
nectar
MAT:0000349
sepal
MAT:0000355
CS57663
James Malone
CS57663 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158687&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158687&type=germplasm
classical Hodgkin's lymphoma
C7164
R46
SALK_037727
James Malone
SALK_037727 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=germplasm&id=4640315
Germplasm:4640315
embryonic cuprophilic cell
FBbt:00005625
bone marrow
MAT:0000084
plant sperm
MAT:0000218
psychiatric disorder
James Malone
A major affective disorder marked by severe mood swings (manic or major depressive episodes) and a tendency to remission and recurrence.
NCI Metathesaurus: C34423
GM12156
leaf
MAT:0000234
Beas2B
platform
The specific version (such as manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment.
cancer site
Location of cancer, primary or metastatic
sensory bristle
MAT:0000152
cervical carcinoma
DOID:2893
corpus cardiacum
FBbt:00001717
compound based treatment
PAC2
uterus
uterine horn
MAT:0000127
temporal lobe
MAT:0000508
hypothalamus
NCI Thesaurus: C22616
MAT:0000112
environmental factor
environment factor
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
cardiovascular disease
James Malone
DOID:1287
medullary breast carcinoma
DOID:5605
GM12875
phenotypic factor
smooth muscle
MAT:0000303
spleen
MAT:0000085
immunoprecipitate
The antibody used to precipitate an antigen out of a solution during the process of immunoprecipitation.
diaphragm
MAT:0000502
type II diabetes mellitus
diabetes mellitus type 2
DOID:9351
plant fluid
MAT:0000347
BEAS-2B
angioimmunoblastic T-cell lymphoma
NCI Thesaurus: C7528
bud
MAT:0000229
embryonic esophagus
FBbt:00005612
chronic obstructive pulmonary disease
DOID:3083
CS57664
James Malone
CS57664 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158688&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158688&type=germplasm
feather
MAT:0000156
compound
James Malone
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
corpus striatum
dorsal striatum
NCI Thesaurus: C12448
NIH3T3-L1
cytomegalovirus
Human Herpesvirus 5
HCMV
DOID:11259
CNS brain hippocampus MMHCC
Obsolete - term hippocampus already exists
NCI Thesaurus: C22615
rat strain
James Malone
Strain or line specific to rat.
CS57603
James Malone
CS57603 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158627&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158627&type=germplasm
phenotype
James Malone
The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype.
visual cortex
MAT:0000509
cardiomyopathy
DOID:3978
medullary thymic epithelial cell
NCI Thesaurus: C45702
GM12891
spiracle
MAT:0000208
pulmonary hypertension
DOID:6432
anlage in statu nascendi
FBbt:00005413
immune system disease
James Malone
DOID:2914
gall tissue
MAT:0000351
CS57666
James Malone
CS57664 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158690&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158690&type=germplasm
oviduct
fallopian tube
uterine tube
MAT:0000126
flower
MAT:0000231
epidermis
MAT:0000154
MCF7
embryonic foregut
FBbt:00005606
chronic myeloid leukemia
DOID:8552
R18
spermathecum
MAT:0000168
CNS brain striatum MMHCC
NCI Thesaurus: C22622
deafness
DOID:10005
NCI Thesaurus: C27644
corm
MAT:0000368
129P1/ReJ
James Malone
http://jaxmice.jax.org/strain/001137.html
MDAMB157
corpus uteri
NCI Thesaurus: C12316
GM12892
plasma cell
multiple myeloma tumour cell
CL:0000786
ventricle
cardiac ventricle
NCI Thesaurus: C12730
MAT:0000497
CS57606
James Malone
CS57606 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158630&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158630&type=germplasm
occipital lobe
occipital cortex
MAT:0000507
pharyngula stage
The pharyngula is a developmental stage in embryonic development which follows the blastula, gastrula and neurula stages.
seed coat
MAT:0000228
WKY
James Malone
RGD:61103
vascular tissue
MAT:0000362
antennal primordium1
FBbt:00005510
trachea
MAT:0000137
pulmonary arterial hypertension
cingulate cortex
cingulate cortex homogenate
NCI Thesaurus: C52713
adenohypophysis
ZFA:0001282
embryonic epipharynx
FBbt:00005614
CS57671
James Malone
CS57671 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158695&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158695&type=germplasm
pigment
pigmentation
MAT:0000159
PC12
vagina
MAT:0000128
CS57610
James Malone
CS57610 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158634&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158634&type=germplasm
animal reproductive system
genital system
MAT:0000305
Down Syndrome
Down's syndrome
trisomy 21 syndrome
DOID:14250
olfactory lobe
olfactory bulb
NCI Thesaurus: C22619
MAT:0000116
cortex
NCI Thesaurus: C12443
H209
C57BL/6J
C57BL6
James Malone
A/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000664.html
JAX:000664
storage organ
MAT:0000366
phyllodes tumor
DOID:2608
cardiac myocyte
CL:0000746
pharyngula high-pec
ZFS:0000032
parietal lobe
MAT:0000506
apical root meristem
MAT:0000220
Dahl salt-sensitive
James Malone
RGD:1582190
lung
MAT:0000135
cleavage stage
antennal primordium2
FBbt:00005537
chronic pancreatitis
DOID:13315
nail
claw
MAT:0000158
MDAMB134VI
embryonic esophageal ganglion
FBbt:00005670
cotyledon
MAT:0000359
GM12716
dose
The total quantity or strength of a substance administered at one time.
hair
vibrissa
MAT:0000160
CS57777
James Malone
CS57777 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158801&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158801&type=germplasm
endosperm
MAT:0000227
dilated cardiomyopathy
DOID:12930
larval day 7-13
ZFS:0000039
GM11994
esophageal adenocarcinoma
DOID:4914
host
An animal or plant or part thereof that nourishes and supports a parasite either in a lab or natural environment.
bronchus
MAT:0000133
RAW264.7
follicle cell
CL:0000477
CS57876
James Malone
CS57876 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158900&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158900&type=germplasm
genital system disease
DOID:15
GLI72
CS57511
James Malone
CS57511 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311932.
http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311932
stem
MAT:0000239
vehicle
A carrier or inert medium used as a solvent (or diluent) in which some compound is formulated and or administered.
embryonic corpus allatum
FBbt:00001719
HBL100
regulatory T-cell
pancreatic T regulatory cell
CL:0000815
dorsomedial neurosecretory cell
FBbt:00004011
CS57778
James Malone
CS57778 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158802&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158802&type=germplasm
GM12249
pharyngeal arch
MAT:0000242
virus strain
James Malone
Strain or line specific to virus
gill
MAT:0000134
disease factor
A disease factor is a clinical factor that describes states of disease associated with a particular sample and/or organism.
erythrocyte
CL:0000232
huntington's disease
DOID:12858
GM11995
larval day 21-29
ZFS:0000041
GM06985
genotype
The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.
RKO
experimental factor
Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma
Helen Parkinson
James Malone
An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner.
Helen Parkinson
James Malone
An experimental factor in Array Express.
CS57875
James Malone
CS57875 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158899&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158899&type=germplasm
CS57601
James Malone
CS57601 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158625&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158625&type=germplasm
polycystic ovary syndrome
DOID:11612
fibromatosis
C3042
HMEC
neuroblast (sensu Vertebrata)
adrenal neuroblast
CL:0000337
H720
embryonic central nervous system
FBbt:00001056
CS57779
James Malone
CS57779 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158803&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158803&type=germplasm
dorsal trunk specific anlage
FBbt:00005489
vitamin B12 deficiency
DOID:8459
GM12750
embryonic central brain surface glia
FBbt:00005664
hippocampus
NCI Thesaurus: C22615
MAT:0000114
GM06993
digestive system disease
DOID:27
S2
renal cell carcinoma
DOID:4450
GM12003
ureter
MAT:0000120
THP-1
polymorphonuclear leukocyte
CL:0000041
CS57515
James Malone
CS57515 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311936
http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311936
HepG2
CS57884
James Malone
CS57884 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158908&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158908&type=germplasm
genetic modification
The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.
Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection
neuroblastoma
DOID:769
HCC1143
wash
The process of applying a solvent (e.g. water) or some solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds.
dorsal root ganglion
NCI Thesaurus: C12462
GM12717
embryonic central brain pars intercerebralis
FBbt:00005667
digit
NCI Thesaurus: C40186
S49
SchneiderSL2
renal clear cell carcinoma
DOID:4467
GM06994
urethra
MAT:0000121
morphology
histology
Microscopic morphology of tissues.
essential thrombocythemia
hemorrhagic thrombocythemia
DOID:2224
GM12004
U266
polyp
DOID:3475
CS57512
James Malone
CS57512 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311933
http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311933
genetic trait
Genetic traits are small inherited parts of the phenotype of an organism
CS57883
James Malone
CS57883 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158907&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158907&type=germplasm
follicular thyroid adenoma
follicular adenoma
DOID:6204
HCC1007
CS57783
James Malone
CS57783 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158807&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158807&type=germplasm
HepaRG
neurofibroma
DOID:962
CS57823
James Malone
CS57823 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158847&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158847&type=germplasm
larval day 5
ZFS:0000037
cell line
The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
replicate
A role played by a a biological sample in the context of a microarray experiment where the intent is that biological or technical variation is measured.
CS57595
James Malone
CS57595 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158619&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158619&type=germplasm
CS57644
James Malone
CS57644 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158668&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158668&type=germplasm
epilepsy
DOID:1826
spinal cord
MAT:0000183
MM1
GM12236
well-differentiated_liposarcoma
chromosomal aberration
An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material.
HeLa
dorsal ridge
FBbt:00000090
CS57871
James Malone
CS57871 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158895&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158895&type=germplasm
melanoma
DOID:1909
phloem
MAT:0000364
CFT-2
U373
CS57521
James Malone
CS57521 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=germplasm&id=1005152522
http://www.arabidopsis.org/servlets/TairObject?type=germplasm&id=1005152522
hyperplasia
James Malone
An abnormal increase in the number of (otherwise normal) cells in an organ or a tissue with consequent enlargement.
NCI Thesaurus http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C3113&bookmarktag=2 Date Accessed: 30th October 2007
GM12234
respiratory system disease
DOID:1579
CS57591
James Malone
CS57591 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158615&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158615&type=germplasm
epigenetic status
Epigenetic status describes the imprinting state of a sample. E.g. Loss of imprinting occurs in some tumour cells
Loss of imprinting occurs in some tumour cells
cell property
An attribute of a cell e.g. CD8+
CD8+
CS57770
James Malone
CS57770 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158794&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158794&type=germplasm
well-differentiated_sarcoma
CS57822
James Malone
CS57822 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158846&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158846&type=germplasm
HEK293T
dorsal prothoracic pharyngeal muscle
FBbt:00000489
CS57769
James Malone
CS57769 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158793&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158793&type=germplasm
chronic gastritis
DOID:4032
muscular dystrophy
DOID:9884
CS57870
James Malone
CS57870 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158894&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158894&type=germplasm
larval day 4
ZFS:0000036
CSBwt-rescued fibroblasts
wood parenchyma
MAT:0000365
U87
CS57520
James Malone
CS57520 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311941
http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311941
nutritional disorder
DOID:374
hypertension
DOID:10763
CS57648
James Malone
CS57648 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158672&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158672&type=germplasm
larval day 14-20
ZFS:0000040
CS57598
James Malone
CS57598 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158622&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158622&type=germplasm
CS57541
James Malone
CS57541 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158565&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158565&type=germplasm
CS57825
James Malone
CS57825 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158849&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158849&type=germplasm
epithelial cell of lung
alveolar epithelial type I
alveolar epithelial type II
bronchial epithelial
bronchial epithelial cells
bronchoalveolar lavage cell
CL:0000082
hydrostatic pressure
James Malone
The pressure exerted by a liquid as a result of its potential energy, ignoring its kinetic energy.
caudate nucleus
NCI Thesaurus: C12451
disease free survival
Period after successful treatment in which there is no appearance of the symptoms or effects of the disease.
rheumatoid arthritis
DOID:7148
GM12248
CS57771
James Malone
CS57771 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158795&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158795&type=germplasm
white blood cell
CL:0000738
limb-girdle muscular dystrophy
Erb's muscular dystrophy
DOID:11724
chronic granulomatous disease
DOID:3265
dorsal pharyngeal muscle primordium
FBbt:00005498
Arabidopsis thaliana strain
James Malone
Strain or line specific to Arabidopsis thaliana.
HEK-293H
U937
xylem
MAT:0000363
GLI56
CS57874
James Malone
CS57874 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158898&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158898&type=germplasm
epithelial cell
epithelial
medullary thymic epithelial cell
oesophageal cell
CL:0000066
CS57596
James Malone
CS57596 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158620&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158620&type=germplasm
CS57646
James Malone
CS57646 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158670&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158670&type=germplasm
larval day 6
ZFS:0000038
CS57824
James Malone
CS57824 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158848&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158848&type=germplasm
risk status
The probability that an event will occur generally with unfavorable outcome.
cell factor
CS57537
James Malone
CS57537 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311958
http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311958
CS57776
James Malone
CS57776 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158800&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158800&type=germplasm
GM12239
R8
972h-
James Malone
972h- is a yeast strain as described in article PMID 12753
PMID: 12753
embryonic corpus cardiacum
FBbt:00001720
HEK293
CS57873
James Malone
CS57873 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158897&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158897&type=germplasm
chronic myelogenous leukemia
CML
DOID:8552
lipoma
DOID:9291
dorsal metathoracic disc
FBbt:00001779
B-2 B cell
large pre-BII cell
small pre-BII cell
CL:0000822
hyperglycemia
hyperglycaemia
DOID:4195
bark
MAT:0000360
GLI60
UACC812
UBOC1
SUM1315MO2
FUM1
James Malone
FUM1 is a yeast strain as described in http://www.genedb.org/genedb/Search?organism=cerevisiae&name=YPL262W&isid=true
http://www.genedb.org/genedb/Search?organism=cerevisiae&name=YPL262W&isid=true
adductor mandibulae complex
ZFA:0000311
B-precursor acute lymphoblastic leukemia
extraction protocol
The procedure used to obtain something from a mixture or compound by chemical or physical or mechanical means, e.g. DNA/RNA extraction
DNA/RNA extraction
mouth
oral cavity
MAT:0000038
HCC70
environmental stress
Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. change in temperature, change in watering regime
change in temperature, change in watering regime
number of injections
The scalar number of injections administered to a material or organism.
T-cell lymphoblastic lymphoma
metabolomic profiling
metabolimic profiling
An experiment in which one or more metabolites are analysed.
ArrayExpress production team
CS57717
James Malone
CS57717 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158741&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158741&type=germplasm
B6.Cg-Tg(SOD1-G93A)1Gur/J
James Malone
B6.Cg-Tg(SOD1-G93A)1Gur/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/004435.html
JAX:004435
CS57583
James Malone
CS57583 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158607&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158607&type=germplasm
invertebrate ganglion
MAT:0000207
subarachnoid hemorrhage
ischaemia
DOID:11236
CS57827
James Malone
CS57827 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158851&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158851&type=germplasm
craniofacial tissue
MAT:0000017
diabetes mellitus
DOID:9351
liver and biliary system
MAT:0000024
Ewing's sarcoma
DOID:3369
blastula dome
ZFS:0000015
adenocarcinoma
James Malone
A type of carcinoma derived from glandular tissue or in which tumor cells form recognizable glandular structures.
CRISP Thesaurus 2006, Term Number 2000-0386, http://crisp.cit.nih.gov/Thesaurus/00000107.htm Date accessed: 1st Novemeber 2007
ear
auditory system
MAT:0000138
B-cell acute lymphoblastic leukemia
B-ALL
DOID:7061
HCC38
129X1/SvJ
129X1
James Malone
129X1/SvJ is a substrain of the mouse strain 129 as described in Jackson Laboratory http://jaxmice.jax.org/strain/000691.html Note this strain was formerly called 129X1
http://jaxmice.jax.org/strain/000691.html
T cell
Th1
Th2
pancreatic T effector cell
CL:0000084
microRNA profiling
An experiment in which a microRNA array is used to analyse the microRNA component of the transcriptome.
ArrayExpress production team
nutrients
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
chow, fertilizer, DEMM 10%FBS
CS57719
James Malone
CS57719 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158743&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158743&type=germplasm
hatching pec-fin
ZFS:0000034
C3H/HeJ
James Malone
C3H/HeJ is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000659.html
JAX:000659
CS57581
James Malone
CS57581 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158605&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158605&type=germplasm
CS57826
James Malone
CS57826 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158850&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158850&type=germplasm
stroke
ischaemia
DOID:3455
digestive system component
MAT:0000018
CAMA1
hypertrophic cardiomyopathy
DOID:11984
129xC57BL/6
129xC57BL/6
James Malone
129xC57BL/6 is a substrain of the mouse strain 129 as described in article PUBMED ID 15015938
PUBMED ID: 15015938
eye
visual system
MAT:0000140
B-cell chronic lymphocytic leukemia
DOID:1040
keratinizing squamous cell carcinoma
DOID:5521
familial combined hyperlipidemia
DOID:13809
GABAergic neuron
CL:0000617
adenohypophyseal placode
ZFA:0001198
T cell acute lymphoblastic leukemia
DOID:5603
media
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil).
liquid, agar, soil
CS57722
James Malone
CS57722 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158746&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158746&type=germplasm
re-sequencing
An experiment in which re-sequencing technology (Solexa/454) is used to generate sequence which can be used to determine nucleic acid sequence, analyse the transcibed regions of the genome, or to quantitate transcript abundance
ArrayExpress production team
GM11832
observation
The act of regarding attentively and studying facts and occurrences, gathering data through analyzing, measuring, and drawing conclusions
CS57834
James Malone
CS57834 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158858&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158858&type=germplasm
epigenetic factor
glial cell (sensu Vertebrata)
CL:0000243
CS57587
James Malone
CS57587 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158611&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158611&type=germplasm
somatic nervous system
somatic PNS
MAT:0000099
survival probability
The probabilty of continuance of life or existence especially under adverse conditions; Probably need a parent survival metric or similar
CC531
immature B cell
CL:0000816
B-cell lymphoma
C3457
colorectal carcinoma
BALB/c
James Malone
BALB/c is a mouse strain of albion mice.
http://en.wikipedia.org/wiki/BALB/c
kaposi's sarcoma
DOID:8632
nose
olfactory system
MAT:0000139
facioscapulohumeral muscular dystrophy
DOID:11727
mature B cell
721 B lymphoblasts
CL:0000785
Fischer 344
F344
James Malone
Fisher344 is a rat strain as described in http://www.ratmap.org/ShowStrainDetails.html?strain=72
http://www.ratmap.org/ShowStrainDetails.html?strain=72
epiblast cell
epiblast stem cell
primary lymphatic endothelial cell
CL:0000352
survival
CS57828
James Malone
CS57828 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158852&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158852&type=germplasm
GM11839
peripheral nervous system
PNS
MAT:0000338
glioblastoma
DOID:3068
animal developmental tissue
MAT:0000019
CS57586
James Malone
CS57586 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158610&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158610&type=germplasm
CS57727
James Malone
CS57727 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158751&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158751&type=germplasm
juvenile dermatomyositis
DOID:14203
Goto-Kakizaki
James Malone
Goto-Kakizaki is a rat strain as described in http://www.taconic.com/wmspage.cfm?parm1=757
http://www.taconic.com/wmspage.cfm?parm1=757
monoclonal gammopathy
monoclonal gammopathy of uncertain significance
DOID:7442
B-lymphocyte
NCI Thesaurus: C12474
BALB/cByJ
James Malone
BALB is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/001026.html
http://jaxmice.jax.org/strain/001026.html
blastula 256-cell
ZFS:0000009
CS57836
James Malone
CS57836 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158860&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158860&type=germplasm
CS57890
James Malone
CS57890 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158914&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158914&type=germplasm
feature extraction
The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification
GM11881
glaucoma
DOID:1686
diffuse_large_B-cell_lymphoma
B-cell lymphoma dlbcl
C3457
oral squamous cell carcinoma
appendix
MAT:0000287
neuron
primary cortex neuron
CL:0000540
gastric carcinoma
gastric cancer
DOID:9138
family history
Relevant aspects of genetic preconditions or family member's clinical history.
C57BL/10
James Malone
C57BL/10 is a mouse strain as described in Jackson Laboratory http://www.informatics.jax.org/searches/reference.cgi?7550
http://www.informatics.jax.org/searches/reference.cgi?7550
mating type a
MO_659
scott syndrome
BY4741
James Malone
CS57886
James Malone
CS57886 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158910&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158910&type=germplasm
SKBR3
glial cell
mixed glial cells
CL:0000125
diffuse scleroderma
DOID:1580
CS57835
James Malone
CS57835 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158859&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158859&type=germplasm
GM11882
CS57714
James Malone
CS57714 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158738&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158738&type=germplasm
ischaemia
ischaemia
DOID:326
myelodysplastic syndrome
neuronal stem cell
neural stem progenitor cell
CL:0000047
asthma
DOID:2841
blastula 512-cell
ZFS:0000010
C57BL/6
James Malone
C57BL/6 is a mouse strain as described in Jackson Laboratory http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml
http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml
undifferentiated sarcoma
DOID:6191
fibroblast
mouse embryonic fibroblast
primary dermal fibroblast
CL:0000057
diabetic nephropathy
DOID:2370
BY4741
James Malone
germ cell tumor
DOID:2994
strain factor
GM11992
SKGT4
genotyping
An experiment in which variation in the genome is analysed
ArrayExpress production team
CS57580
James Malone
CS57580 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158604&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158604&type=germplasm
nevus
An uncommon benign neoplasm arising from the bone. It is characterized by the presence of spindle-shaped or stellate chondrocytes, a lobulated growth pattern, myxoid stroma formation, and sometimes multinucleated giant cells. It has been associated with chromosomal rearrangement of 6q13 and 6q25 bands. The most common clinical symptom is mild, localized pain.
NCI Thesaurus: DOID:2694
stage I endometrioid carcinoma
fat tissue
MAT:0000015
irritable bowel syndrome
DOID:9778
CS57715
James Malone
CS57715 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158739&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158739&type=germplasm
blastula 30%-epiboly
ZFS:0000016
C57BL/6J
James Malone
C57BL/6J is a mouse strain as described in Jackson Laboratory http://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=strains/details&strainid=7
http://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=strains/details&strainid=7
uterine fibroid
An uncommon benign neoplasm arising from the bone. It is characterized by the presence of spindle-shaped or stellate chondrocytes, a lobulated growth pattern, myxoid stroma formation, and sometimes multinucleated giant cells. It has been associated with chromosomal rearrangement of 6q13 and 6q25 bands. The most common clinical symptom is mild, localized pain.
DOID:13223
fetal growth restriction
DOID:13294
strain
this class was originally 'strain or line'
line
James Malone
A population or type of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
diffuse gastric adenocarcinoma
NCI Thesaurus: C9159
brain tumor glioblastoma
DOID:3074
cardiovascular system
MAT:0000016
GM11993
nucleic acid extracted
The type of nucleic acid obtained as a result of following a given protocol.
CS57716
James Malone
CS57716 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158740&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158740&type=germplasm
methylation profiling
Methylation specific oligonucleotide microarray
An experiment in which the methylation state is determined and is compared between samples.
ArrayExpress production team
Duchenne muscular dystrophy
DOID:11723
stage II endometrioid carcinoma
irradiate
The treatment of a material with radiation
aorta
NCI Thesaurus: C12669
MAT:0000035
infiltrating ductal carcinoma
Made obsolete: considered as synonym to invasive ductal carcinoma
appendage
MAT:0000023
clinical factor
James Malone
A clincal factors is a biomaterial factor that concerns the observation, treatment or measurement of disease within subjects.
age
James Malone
The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).
3 days post planting
lymphoma
DOID:353
ejaculatory duct
MAT:0000170
carotid artery
MAT:0000501
retina
MAT:0000142
fetus
embryo late (growth) stage
MAT:0000399
cranial ganglion
head ganglion
cranial ganglia
mononuclear cell
CL:0000842
adaxial cells
ZFA:0000003
cleavage 2-cell
ZFS:0000002
spondyloarthropathy
DOID:1123
beta cell
beta cell islets
NCI Thesaurus: C32199
lymph
MAT:0000055
ganglion
MAT:0000343
congenital bilateral absence of the vas deferens
James Malone
Congenital bilateral absence of the vas deferens (CAVD) is a condition in which the two vas deferens, male reproductive organs, fail to form properly prior to birth.
Wikipedia: http://en.wikipedia.org/wiki/Congenital_absence_of_the_vas_deferens
Drosophila C virus
NCI Metathesaurus: C0318594
aortic stenosis
DOID:1712
infiltrating lobular carcinoma
Made obsolete: considered as synonym to invasive lobular carcinoma
clear cell sarcoma of the kidney
DOID:4880
macrophage
bone marrow-derived macrophage
monocyte-derived macrophage
CL:0000235
salivary gland
MAT:0000079
testis
male gonad
testicle
MAT:0000131
malignant pleural mesothelioma
DOID:7474
cranium
gustatory system
MAT:0000340
adult muscle precursor primordium
FBbt:00005516
monophasic synovial sarcoma
DOID:5495
cleavage 32-cell
ZFS:0000006
acute quadriplegic myopathy
NCI Metathesaurus: C1406910
trigeminal ganglion
MAT:0000511
fertilized egg stage
zygotel
ZFS:0000001
MAT:0000074
squamous cell carcinoma
squamous cell cancer
DOID:1749
biomaterial factor
haemopoietic system
hematological system
MAT:0000022
lymph node
MAT:0000442
compound factor
anthrax
DOID:7427
blood vessel
MAT:0000393
pharyngeal nervous system
MAT:0000341
hepatocellular carcinoma
HCC
hepatoma
NCI Thesaurus: C3099
independent continuant
A continuant [snap:Continuant] that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
An organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
anterior spiracle specific anlage
FBbt:00005487
sperm
spermatazoon
male gamete
MAT:0000131
taste system
gustatory system
MAT:0000275
prostate
MAT:0000078
male germ cell
testis - germ cell
CL:0000015
adult midgut precursor
FBbt:00000449
acute promyelocytic leukemia
APML
NCI Thesaurus: C3182
segmentation 26+ somites
ZFS:0000028
Dahl salt-resistant
James Malone
RGD:1582184
basal ganglion
MAT:0000450
behavioural stimulus
A treatment applied to a sample where some behaviour is expected as a result e.g. avoidance
avoidance
motoneuron
lateral motoneuron
medial motoneuron
CL:0000100
human granulocytic anaplasmosis
Human granulocytic ehrlichiosis
NCI Metathesaurus: C0483368
MedlinePlus: 001381
CS57785
James Malone
CS57785 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158809&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158809&type=germplasm
gland
exocrine system
MAT:0000021
blastula sphere
ZFS:0000014
somatic cell
NCI Thesaurus: C12949
Hodgkin's lymphoma
DOID:353
Aeromonas hydrophila infection
Aeromonas hydrophila infection is a bacterial disease caused by infection from the Aeromonas hydrophila bacteria.
NCI Metathesaurus: C0085491
antibody
James Malone
Infection-fighting protein molecule in blood or secretory fluids that tags, neutralizes, and helps destroy pathogenic microorganisms such as bacteria, viruses and toxins.
epididymus
MAT:0000130
malpighian tubule
MAT:0000123
FBbt:00005725
material type
Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell
population of an organism, organism, organism part, cell
Okamoto-Aoki
James Malone
RGD:1581618
pituitary
MAT:0000077
globus pallidus
MAT:0000510
benign prostatic hyperplasia
James Malone
DOID:11131
segmentation 20-25 somites
ZFS:0000027
acute myelomonocytic leukemia
AMML
Acute M4 Myeloid Leukemia
NCI Thesaurus: C7463
myocardium
MAT:0000453
neural crest cell
CL:0000333
129 mouse strain
129 is a mouse strain as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
Simpson E. M., Linder C. C., Sargent E. E., Davisson M. T., Mobraaten L. E., and Sharp J. J. (1997) Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice. Nature Genet. 16, 19-27.
http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
spindle cell tumor
DOID:2414
somatic nervous system
MAT:0000342
CS57789
James Malone
CS57789 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158813&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158813&type=germplasm
animal fluid
MAT:0000020
lymphatic system
MAT:0000197
cleavage 16-cell
ZFS:0000005
Syracuse Low Avoidance
James Malone
RGD:1578703
islet of Langerhans
ductus deferens
MAT:0000129
apical shoot meristem
MAT:0000224
A/J
James Malone
A/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000646.html
http://jaxmice.jax.org/strain/000646.html
anterior endoderm primordium
FBbt:00005524
lung carcinoma
DOID:3905
Whipple's disease
DOID:8476
HIV-1
HIV-1 seropositive
NCI Thesaurus: C14220
lobular breast carcinoma
DOID:3457
enteric nervous system
enteric PNS
MAT:0000102
Burkitt's lymphoma
DOID:8584
entity
fin
MAT:0000087
bipolar disorder
DOID:3312
blastula oblong
ZFS:0000013
CS57896
James Malone
CS57896 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158920&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158920&type=germplasm
artery
arterial system
MAT:0000034
129S6
129S6/SvEvTac
James Malone
129S6 is a substrain of the mouse strain 129 as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
control spike calibration
A Reporter that could be hybridized to an exogenously added nucleic acid or protein (spike) before or during hybridization and is used as a control for data processing.
acute myeloid leukemia
AML
DOID:9119
sampling time
adult segment
MAT:0000271
pharynx
MAT:0000049
lateral shoot meristem
MAT:0000225
endometrium
MAT:0000319
pancreas
MAT:0000075
Syracuse High Avoidance
James Malone
RGD:1578695
memory impairment
NCI Metathesuarus: C55427
anterior midgut primordium
FBbt:00000444
lung adenocarcinoma
DOID:3910
Caco-2
vertebrate limb
vertebrata limb
MAT:0000090
tuberculosis
DOID:399
head and neck squamous cell carcinoma
DOID:5520
periodontitis
DOID:824
bronchoalveolar adenocarcinoma
DOID:4926
ventral nerve cord
MAT:0000339
blastula stage
MAT:0000396
white fat
MAT:0000199
CS57901
James Malone
CS57901 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158925&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158925&type=germplasm
acute monoblastic leukaemia
DOID:8864
conjunctiva
NCI Thesaurus: C12341
129/Sv
James Malone
129/Sv is a substrain of the mouse strain 129 as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
Alzheimer's disease
DOID:10652
SALK_049497
James Malone
SALK_049497 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=germplasm&id=4652085
Germplasm:4652085
oesophagus
esophagus
MAT:0000048
scale
MAT:0000257
lymphoblast
NCI Thesaurus: C13013
alveolar rhabdomyosarcoma
DOID:4051
mammary gland
MAT:0000073
Wistar-Kyoto
James Malone
RGD:1359002
sample factor
period of infection
sympathetic nervous system
sympathetic PNS
MAT:0000100
tumor
tumour
An abnormal mass of tissue that results from excessive cell division. Tumors perform no useful body function. They may be benign (not cancerous) or malignant (cancerous).
NCI Metathesaurus
Breast_Tumor_Luminal
temporal lobe epilepsy
DOID:3328
C2C12
dorsal mesothoracic disc
FBbt:00001778
vein
venous system
MAT:0000037
lymph vessel
lymphatic vessel
MAT:0000443
biopsy number
radicle
MAT:0000415
squamous cell lung carcinoma
DOID:3907
CS57641
James Malone
CS57641 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158665&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158665&type=germplasm
Canton S
Canton-S
James Malone
FBst0000001Â
intestine
gut
MAT:0000043
acute lymphocytic leukemia
ALL
DOID:9952
dorsal root ganglion
spinal ganglion
MAT:0000162
congestive heart failure
DOID:395
lymphocyte
CL:0000542
aicardi syndrome
DOID:8461
folate deficiency
folic acid deficiency
DOID:8453
anterior endoderm anlage in statu nascendi
FBbt:00005418
Copenhagen
James Malone
RGD:1358153
sampling site
parasympathetic nervous system
parasympathetic PNS
MAT:0000101
performer
An individual who does some experimental process.
pneumococos infection
DOID:9805
CS57758
James Malone
CS57758 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158782&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158782&type=germplasm
ulcerative colitis
DOID:8577
embryonic gastric caecum
FBbt:00005629
heart
MAT:0000036
blastula high
ZFS:0000012
congestive cardiomyopathy
DOID:12930
antenna
MAT:0000086
biopsy site
The physical site from which tissue has been removed from a living organism.
stem cell
adipose tissue-derived stem cell
conditioned mesenchymal stem cell
mesenchymal stem cell
CL:0000034
gall bladder
MAT:0000072
Drosophila melanogaster strain
James Malone
Strain or line specific to Drosophila melanogaster
tongue
MAT:0000040
body ganglion
trunk ganglion
MAT:0000344
cockayne syndrome
DOID:2962
CS57631
James Malone
CS57631 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158655&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158655&type=germplasm
corpus allatum
FBbt:00001716
MAT:0000210
adrenal medulla
MAT:0000495
embryonic central brain
FBbt:00005662
translation profiling
A translation profiling is an experiment type in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
United States Patent 20040023256
hindbrain
rhombencephalon
MAT:0000107
juvenile days 45-89
ZFS:0000043
HCC1500
dermatomyositis
DOID:10223
borderline leprosy
DOID:1023
breast carcinoma
DOID:3459
portal hypertension
ischaemia
DOID:10762
GM12761
stylopod
The proximal part of the limb (e.g. between shoulder and elbow)
MAT:0000093
BT549
cellular modification
The act of alteration or modification of a cell e.g. RNAi
RNAi
percent oxygen concentration
ovarian carcinoma
CS57706
James Malone
CS57706 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158730&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158730&type=germplasm
thorax
MAT:0000295
root nodule
MAT:0000353
embryonic specific part
An embryonic specific part is an organism part which is specific to embryos.
Met5A
Wistar-Furth
James Malone
RGD:1357955
embryonic central brain glia
FBbt:00005663
male inflorescence
MAT:0000316
CS57637
James Malone
CS57637 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158661&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158661&type=germplasm
coronary artery disease
DOID:3363
duodenum
MAT:0000044
larval stage
MAT:0000400
HCC1569
substantia nigra
MAT:0000504
tuberculoid leprosy
DOID:1025
developmental stage
A developmental stage is some identifiable period in an organism's life cycle e.g. puberty
puberty
bladder
MAT:0000122
NCI Thesaurus: C12414
BT483
porphyria
DOID:13268
GM12762
breast adenocarcinoma
DOID:3458
percent oxygen
cell type
The type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.
epithelial, glial.
head
MAT:0000294
CS57709
James Malone
CS57709 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158733&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158733&type=germplasm
Pseudomonas infection
DOID:2903
cochlear hair cell
CL:0000202
Wistar
James Malone
RGD:10044
root cap
MAT:0000357
embryonic stem cell
CL:0000352
cornea
NCI Thesaurus: C12342
caecum
MAT:0000288
tail
MAT:0000094
female inflorescence
MAT:0000317
CS57629
James Malone
CS57629 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158653&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158653&type=germplasm
MDAMB468
embryonic central brain mushroom body
FBbt:00005666
stigma
MAT:0000524
HCC1187
mushroom body
MAT:0000336
juvenile stage
MAT:0000402
pathogen test
Tests and results for pathogens infecting organism from which the biosource is derived
dendritic cell
CL:0000451
cerebellum
cerebellum peduncles
NCI Thesaurus: C12445
autopod
hand
paw
foot
The generic name for hand, paw, foot, etc.
MAT:0000091
occurrent
An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
The life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
bronchial epithelium
C32231
population
The total number of individuals inhabiting a particular region or area.
GM12751
TBP-105Q
James Malone
TBP-105Q is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/008075.html
JAX:8075Â Â Â Â
Emery-Dreifuss muscular dystrophy
DOID:11726
cochlea
MAT:0000144
NCI Thesaurus: C12395
obesity
DOID:9970
tuber
MAT:0000358
CS57704
James Malone
CS57704 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158728&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158728&type=germplasm
phyllid
MAT:0000276
skin
MAT:0000284
conventional clear cell renal carcinoma
DOID:4467
embryonic central brain neuron
FBbt:00005665
leprosy
DOID:1024
CS57630
James Malone
CS57630 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158654&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158654&type=germplasm
MDAMB453
medulla oblonmgata
MAT:0000111
HCC1428
dermal neurofibroma
A dermal neurofibroma is a neurofibroma that occurs in situ of the skin.
central nervous system cancer
NCI Thesaurus: C4627
juvenile days 30-44
ZFS:0000042
pathogen
A biological agent that causes disease or illness to its host
BT474
B6C3F1
James Malone
B6C3F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100010.html
JAX:100010
pool
A mix of specimens from multiple individuals.
GM12760
zeugopod
The middle part of the limb (e.g. between the elbow and wrist)
MAT:0000092
breast tumor luminal
emphysema
NCI Thesaurus: C3348
clypeo-labral primordium
FBbt:00005538
CS57705
James Malone
CS57705 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158729&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158729&type=germplasm
morbid obesity
DOID:11981
cambium
MAT:0000223
microglial cell
mixed glial cells (predominantly microglia)
CL:0000129
cerebrospinal fluid
NCI Thesaurus: C12692
accumbens nucleus
MAT:0000512
parietal cell
CL:0000162
bone marrow MMHCC
NCI Thesaurus: C22552
pronephros
MAT:0000117
root
MAT:0000005
ZR751
leaf vascular tissue
MAT:0000276
carpel
MAT:0000516
CS57627
James Malone
CS57627 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158651&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158651&type=germplasm
MDAMB436
dedifferentiated chondrosarcoma
DOID:5864
HCC202
endocarditis
DOID:10314
adult hindgut precursor
FBbt:00005646
clinical treatment
The current clinical treatment(s) of the patient from which the biosource is derived. E.g. radiotherapy
radiotherapy
female reproductive system
female genital system
MAT:0000028
dependent continuant
Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
bladder mucosa
NCI Thesaurus: C32205
intracranial hemorrhage NOS
DOID:1126
Rett syndrome
Rett disorder
DOID:1206
array design
Descriptions pertaining to the design of the array.
pelvic girdle
MAT:0000182
BT20
papillary thyroid carcinoma
DOID:3969
cerebral cortex
brain cortex
NCI Thesaurus: C12443
MAT:0000108
caudate nucleus
MAT:0000513
delivery method
Method used to deliver e.g. a compound or solution for treatment.
a compound or solution for treatment.
mitochondrial disorder
hyperglycaemia
DOID:700
BJABK3
pars intercerebralis
MAT:0000337
pretreatment
bone marrow
Duplicate term : see bone marrow EFO_0000868
NCI Thesaurus: C12431
CS57628
James Malone
CS57628 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158652&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158652&type=germplasm
MDAMB435
Was originally considered to be a breast cancer cell line but has since been identified as a melanoma cell line.
stomatal complex
MAT:0000346
plant ovary
MAT:0000517
gametophyte
MAT:0000004
ZF4
HCC2157
adult foregut precursor
FBbt:00005611
clinical information
endometrioid carcinoma
DOID:3000
abdomen
MAT:0000298
lateral root meristem
MAT:0000221
bladder tumor
DOID:5428
pectoral girdle
MAT:0000181
interneuron
GABAergic interneuron
CL:0000099
BL41K3
papillary renal cell carcinoma
DOID:4465
CS57625
James Malone
CS57625 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158649&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158649&type=germplasm
brain tumor glioblastoma
preeclampsia
ischaemia
DOID:10591
mixed lobular and ductal breast carcinoma
DOID:6582
central nervous system
neuraxis
MAT:0000457
HCC1937
CS57543
James Malone
CS57543 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158567&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158567&type=germplasm
damage response
Physiological response to e.g. leaf's response to physical damage by a caterpillar on a plant leaf
leaf's response to physical damage by a caterpillar on a plant leaf
MDAMB415
WI38
seedhead
MAT:0000237
penis
MAT:0000186
kidney
metanephros
MAT:0000119
CS57710
James Malone
CS57710 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158734&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158734&type=germplasm
taproot
MAT:0000222
neck
MAT:0000297
clinical history age
The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage.
endothelial cell
lymphatic endothelial cell
primary lymphatic endothelial cell
CL:0000115
adult eye primordium
FBbt:00005515
cartilage
MAT:0000189
bacterial disease
James Malone
A bacterial disease is a disease factor that is caused primarily by bacteria.
Pseudomonas aeruginosa CF5 infection
A Pseudomonas aeruginosa CF5 infection is a Pseudomonas infection of strain CF5.
Y. Apidianakis, M.N. Mindrinos, W. Xiao, G.W. Lau, R.L. Baldini, R.W. Davis and L.G. Rahme, Profiling early infection responses: Pseudomonas aeruginosa eludes host defenses by suppressing antimicrobial peptide gene expression, Proc. Natl. Acad. Sci. USA 102 (2005), pp. 2573–2578
apical meristem
PO:0020148
bladder MMHCC
NCI Thesaurus: C22729
invasive lobular carcinoma
infiltrating lobular carcinoma
DOID:3460
pre-B cell
B-cell precursor
pre-BI cell
CL:0000817
brain structure
brain
NCI Thesaurus: C12439
MAT:0000098
CS57626
James Malone
CS57626 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158650&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158650&type=germplasm
HCC1954
forebrain
MAT:0000105
monocyte
naive
CL:0000576
data transformation
James Malone
A manipulation, alteration or processing of the original raw data to produce a new otherwise alternative view.
MDAMB361
embryonic brain
FBbt:00001060
stamen
MAT:0000515
seminal vesicle
MAT:0000171
mesonephros
MAT:0000118
root hair
MAT:0000352
environment
Synonym of environmental factor
James Malone
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
clinical history
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
trunk
MAT:0000296
Pseudomonas aeruginosa PA14 infection
A Pseudomonas aeruginosa PA14 infection is a Pseudomonas infection of strain PA14.
Plotnikova, J. M., Rahme, L. G., Ausubel, F. M. (2000). Pathogenesis of the Human Opportunistic Pathogen Pseudomonas aeruginosa PA14 in Arabidopsis. Plant Physiol. 124: 1766-1774
apoptotic amnioserosa
FBbt:00005556
bladder carcinoma
DOID:4007
joint
MAT:0000188
invasive ductal and lobular carcinoma
DOID:6583
SUM44PE
dorsal epidermis primordium
FBbt:00005526
sarcoidosis
DOID:11335
CS57677
James Malone
CS57677 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158695&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158701&type=germplasm
axial skeleton
MAT:0000148
individual
is equivalent to an instance of class organism
Identifier or name of the individual organism from which the biomaterial was derived.
Brown-Norway
BN
James Malone
Brown-Norway is a rat strain as described in http://www.informatics.jax.org/external/festing/rat/docs/BN.shtml
http://www.informatics.jax.org/external/festing/rat/docs/BN.shtml
proteomic profiling
An experiment where proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling
ArrayExpress production team
Antibody profiling experiment
embryonic anal pad
FBbt:00005748
bone
NCI Thesaurus: C12366
MAT:0000299
damage intensity
Measurement of physical damage, e.g. by a caterpillar on a plant leaf
by a caterpillar on a plant leaf
embryonic frontal ganglion
FBbt:00005668
operator variation
The effects of different investigators, laboratories, or organizations on experimental results are studied.
female
CARO:0000028
CS57624
James Malone
CS57624 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158648&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158648&type=germplasm
LY2
CS57850
James Malone
CS57850 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158874&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158874&type=germplasm
granulocyte
CL:0000094
primordial germ cell
CL:0000670
individual genetic characteristic
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
craniofacial skeleton bone
MAT:0000149
SUM52PE
dorsal histoblast nest abdominal
FBbt:00001791
antigen profiling
An experiment where an antigen array is used (antigens deposited on the array) to detect, quantify or otherwise analyse antibodies in solution.
ArrayExpress production team
organism
The genus and species (and subspecies) of the organism from which the biomaterial is derived from. E.g Drosophila melanogaster
Drosophila melanogaster
embryonal rhabdomyosarcoma
DOID:3246
CNS brain cerebellum MMHCC
NCI Thesaurus: C22609
CS57735
James Malone
CS57735 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158759&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158759&type=germplasm
embryonic foregut sensory structure
FBbt:00005616
blood vessel endothelial cell
primary blood vessel endothelial cell
primary microvascular endothelial cell
umbilical vein endothelial cell
CL:0000071
cystic fibrosis
DOID:1485
L3055
male
CARO:0000027
pertussis
whooping cough
DOID:1116
CS57848
James Malone
CS57848 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158872&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158872&type=germplasm
growth condition
I think this is a role that an environmental factor can take
A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.
CS57572
James Malone
CS57572 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158596&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158596&type=germplasm
exoskeleton
MAT:0000150
childhood acute myeloid leukemia
NIC Thesaurus: C9160
infection
The state of being infected such as from the introduction of a foreign agent such as serum, vaccine, antigenic substance or organism.
GM12146
dorsal imaginal precursor
FBbt:00005831
SUM190PT
head disease
The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed. E.g Acute Lymphocytic Leukemia
DOID:4149
GM11830
blood
peripheral blood
peripheral blood progenitor
whole blood
blood cells
NCI Thesaurus: C12434
MAT:0000083
GM12872
B lymphocyte
CL:0000236
ZR7530
oligoastroglioma
DOID:7912
HCC3153
CS57570
James Malone
CS57570 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158594&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158594&type=germplasm
CS57847
James Malone
CS57847 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158871&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158871&type=germplasm
calpainopathy
limb-girdle muscular dystrophy type 2A
DOID:11724
extra-adrenal sympathetic paraganglioma
NCI Thesaurus: C48576
chondroblastoma
DOID:2649
infertility
sterile
DOID:5223
GM12154
limb bone
limb skeleton
MAT:0000151
hematological neoplasm
haematological neoplasm
DOID:253
GM11831
SUM225CWN
CS57569
James Malone
CS57569 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158593&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158593&type=germplasm
blastocyst
NCI Thesaurus: C13739
GM12815
embryonic antennal sense organ
FBbt:00005568
Becker's muscular dystrophy
Benign pseudohypertrophic muscular dystrophy
DOID:9884
obsolete class
oligodendroglioma
DOID:3181
HCC2185
embryonic ganglion mother cell
FBbt:00001433
CS57843
James Malone
CS57843 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158867&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158867&type=germplasm
cancer
James Malone
A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease.
ductal carcinoma in situ
ZR75B
MDAMB231
GM12814
BY5251
James Malone
SUM159PT
prostate adenocarcinoma
prostate cancer
DOID:2526
CS57701
James Malone
CS57701 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158725&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158725&type=germplasm
CS57563
James Malone
CS57563 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311984
http://www.arabidopsis.org/servlets/TairObject?type=stock&id=1000311984
external control ratio
Use of spiked in controls in a measurement of the spiked in external/internal ratio
CS57801
James Malone
CS57801 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158825&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158825&type=germplasm
chondromyxoid fibroma
James Malone
An uncommon benign neoplasm arising from the bone. It is characterized by the presence of spindle-shaped or stellate chondrocytes, a lobulated growth pattern, myxoid stroma formation, and sometimes multinucleated giant cells. It has been associated with chromosomal rearrangement of 6q13 and 6q25 bands. The most common clinical symptom is mild, localized pain.
DOID:2694
injury
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity
mating type h minus
MO_407
GM07357
RNAi profiling
RNAi profiling is an experiment type in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
ArrayExpress production team
CS57842
James Malone
CS57842 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158866&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158866&type=germplasm
ecotype
James Malone
A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
the A. thaliana Ecotype Ler
IMR-32
GM12813
B cell
CL:0000236
myeloid cell
CL:0000763
chondrosarcoma
DOID:3371
CS57699
James Malone
CS57699 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158723&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158723&type=germplasm
SUM185PE
CS57560
James Malone
CS57560 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158584&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158584&type=germplasm
protocol
CS57790
James Malone
CS57790 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158814&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158814&type=germplasm
exposure
The act of subjecting someone or something to an influencing experience. E.g. exposure to cigarette smoke
exposure to cigarette smoke
inner cell mass
NCI Thesaurus: C13740
cataract
DOID:83
GM11829
CS57840
James Malone
CS57840 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158864&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158864&type=germplasm
oligoastrocytoma
DOID:7912
IB3-1
duration
ChIP-Chip
An experiment where chromatin immunoprecipitation (ChIP) is used in combination with microarray technology.
<WEB> http://en.wikipedia.org/wiki/ChIP-on-chip
plant embryo
MAT:0000226
MDAMB-157
GM12812
CS57556
James Malone
CS57556 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158580&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158580&type=germplasm
chordoma
DOID:3302
progeria syndrome
DOID:3911
CS57692
James Malone
CS57692 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158716&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158716&type=germplasm
transcription profiling
A transcription profiling is an experiment type in which the transcriptome of a biological sample is analysed.
ArrayExpress production team
tectum
MAT:0000451
glioma
DOID:2627
GM07056
chordotonal organ
MAT:0000209
instrument factor
To be imported from OBI
sensory system disease
James Malone
A sensory system disease is a disease which has as location the sensory system.
hermaphrodite
An organism having both male and female sexual characteristics and organs.
NCI Thesaurus: C45909
Kin-S49
clear cell adenocarcinoma
DOID:4468
idiopathic pulmonary fibrosis
cryptogenic fibrosing alveolitis
NCI Thesaurus: C35716
bone MMHCC
NCI Thesaurus: C22682
SUM149PT
comparative genomic hybridization
An experiment in which changes in DNA sequence copy number are analysed. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
ArrayExpress production team
GM12763
MDAMB175VII
CS57551
James Malone
CS57551 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158575&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158575&type=germplasm
chromophobe renal cell carcinoma
DOID:4471
CS57691
James Malone
CS57691 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158715&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158715&type=germplasm
experimental design
experimental design refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.
prognostic subgroup
A grouping of subjects in some study grouped on the basis of the probable outcome of some disease e.g. by gene expression, by physiological indicators etc
glutamatergic neuron
CL:0000679
GM07345
tegmentum
MAT:0000452
mating type
A mating type is a biomaterial factor which describes the type of sexual reproduction through isogamy occur in eukaryotes that undergo.
tiling path
A tiling path experiment is an experiment type in which a tiling path array (where probes are arrayed covering target regions e.g. a genome or chromosome at very high density) is used to identify transcribed regions.
ArrayExpress production team
insulinoma
DOID:3903
lepromatous leprosy
DOID:10887
lateral line system
MAT:0000249
ectoderm anlage in statu nascendi
FBbt:00005414
clear cell renal carcinoma
DOID:4467
IMR-90
Epstein-Barr virus infection
EBV infection
DOID:2938
tooth
MAT:0000041
HMT3522S1
myxoid liposarcoma
DOID:5363
hereditary leiomyomatosis and renal cell cancer
HLRCC
NCI Thesaurus: C51302
CS57923
James Malone
CS57923 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005164919&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005164919&type=germplasm
GM07034
CS57811
James Malone
CS57811 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158835&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158835&type=germplasm
Hibiscus chlorotic ringspot virus
NCI Metathesaurus: C1017212
GM12043
experiment type
An experiment type is an experimental factor describing the area of technology that was used to perform an experiment.
ChIP-Chip array
CS57752
James Malone
CS57752 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158776&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158776&type=germplasm
CS57549
James Malone
CS57549 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158573&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158573&type=germplasm
treatment
segmentation 10-13 somites
ZFS:0000025
signet ring cell carcinoma
DOID:3493
idiopathic cardiomyopathy
NCI Thesaurus: C53654
narcolepsy
DOID:8986
processual entity
HMEC184
CS57908
James Malone
CS57908 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158932&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158932&type=germplasm
GM07055
fat body sensu invertebrata
MAT:0000096
disease staging
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. E.g. Dukes C stage describing colon cancer
Dukes C stage describing colon cancer
exercise
Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness.
CS57810
James Malone
CS57810 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158834&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158834&type=germplasm
myositis
inflammatory myopathy
DOID:633
GM12044
transfect
The process of bringing about genetic alteration of any cell or organism by a variety of means including recombinant DNA technology, viruses, chemical mutagens and X-rays.
CS57548
James Malone
CS57548 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158572&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158572&type=germplasm
CS57753
James Malone
CS57753 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158777&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158777&type=germplasm
segmentation 14-19 somites
ZFS:0000026
sickle cell disease
DOID:10923
adrenal gland pheochromocytoma
NCI Thesaurus: C3326
stomach
MAT:0000051
HT-29
disease state
The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed. E.g Acute Lymphocytic Leukemia
Acute Lymphocytic Leukemia
fat body sensu amphibia
MAT:0000456
GM07000
CS57905
James Malone
CS57905 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158929&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158929&type=germplasm
CS57807
James Malone
CS57807 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158831&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158831&type=germplasm
CS57544
James Malone
CS57544 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158568&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158568&type=germplasm
Enterococcus faecalis infection
NCI Metathesaurus: C0038404
shear stress
A stress state where the stress is parallel or tangential to a face of the material.
papillary cystadenocarcinoma
DOID:3110
HIV
HIV infection
human immunodeficiency virus
DOID:526
NCI Thesaurus: C3108
event free survival time
myoblast
nonmesodermal cell
CL:0000056
GM12005
acute lymphoblastic leukemia
ALL
DOID:5600
segmentation 1-4 somites
ZFS:0000023
CS57750
James Malone
CS57750 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158774&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158774&type=germplasm
HS578T
larynx
MAT:0000187
myocardial infarction
ischaemia
DOID:5844
brown fat
MAT:0000198
distant metastasis free survival
CS57904
James Malone
CS57904 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158928&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158928&type=germplasm
GM07022
CS57803
James Malone
CS57803 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158827&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158827&type=germplasm
Pectobacterium carotovorum infection
Erwinia carotovora infection
NCI Metathesaurus: C0085485
timepoint
GM12006
event distant metastases
Occurrence of a metastasis measured from some defined time point
AIDS
acquired immune deficiency syndrome
acquired immunedeficiency syndrome
DOID:635
segmentation 5-9 somites
ZFS:0000024
CS57751
James Malone
CS57751 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158775&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158775&type=germplasm
sex
Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
NCI Thesaurus: C28421
smooth muscle cell
primary aortic smooth muscle cell
primary uterine smooth muscle cell
CL:0000192
CS57867
James Malone
CS57867 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158891&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158891&type=germplasm
CS57820
James Malone
CS57820 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158844&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158844&type=germplasm
dorsal apodeme specific anlage
FBbt:00005476
limb bone
limb skeleton
MAT:0000151
chronic lymphocytic leukemia
CLL
DOID:1040
behaviour
The actions or reactions of an object or organism, usually in relation to the environment or surrounding world of stimuli. E.g. Fixed action pattern courtship behaviour in Drosophila. Forager behaviour in honey bees.
Fixed action pattern courtship behaviour in Drosophila. Forager behaviour in honey bees.
nerve cell
neuroblastoma cell
CL:0000540
CS57742
James Malone
CS57742 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158766&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158766&type=germplasm
severe acute respiratory syndrome
DOID:2945
osteosarcoma
DOID:3347
active gastritis
DOID:4029
event death
A permanent cessation of all vital functions; the end of life. Can be applied to a whole organism or to a part of an organism.
liver heptocellular carcinoma
hepatocellular adenoma
NCI Thesaurus: C3758
leydig cell
testis - leydig cell
CL:0000178
time to development of distant metastases
hemopoietic progenitor cell
CL:0000037
GM12144
TERV
CS57859
James Malone
CS57859 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158883&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158883&type=germplasm
small cell lung carcinoma
DOID:5409
plasma cell leukemia
CS57816
James Malone
CS57816 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158840&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158840&type=germplasm
basal breast tumor
basal breast tumor is a high grade, triple-negative breast tumor, i.e. they express no estrogen receptor, progesterone receptor nor Her2/neu proteins.
wikipedia:http://en.wikipedia.org/wiki/Basal-like_carcinoma
cleavage 8-cell
ZFS:0000004
CTL sensitivity
nervous system disease
NCI Thesaurus: C12755
schwannoma
DOID:3192
CS57743
James Malone
CS57743 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158767&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158767&type=germplasm
liver carcinoma
leukocyte
white blood cell
CL:0000738
viral disease
James Malone
A viral disease is a disease factor that is caused primarily by the infection or otherise hosting of a virus.
acute erythroid leukemia
DOID:1239
overall survival
hemopoietic stem cell
hematopoietic stem cell
CL:0000037
time before disease progression
ectoderm
FBbt:00005428
GM12145
time
precursor T lymphoblastic leukemia
CS57858
James Malone
CS57858 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158882&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158882&type=germplasm
skin disease
James Malone
Any deviation from the normal structure or function of the skin or subcutaneous tissue that is manifested by a characteristic set of symptoms and signs.
NCI Thesaurus: C3371
yeast strain
James Malone
Strain or line specific to yeast
CS8581
James Malone
CS8581 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=4473197&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=4473197&type=germplasm
Barrett's esophagus
DOID:9206
cleavage 64-cell
ZFS:0000007
liposarcoma
DOID:3382
natural killer cell
natural killer
CL:0000623
accumbens nucleus
nucleus accumbens core
nucleus accumbens shell
nucleus accumbens whole
NCI Thesaurus: C52733
Kaposi's sarcoma cell
NCI Thesaurus: C9087
CS57737
James Malone
CS57737 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158761&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158761&type=germplasm
schizophrenia
DOID:5419
organism part
The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
tissue, organ, system, sperm, blood or body location (arm).
malignant peripheral nerve sheath tumor
DOID:5940
hepatocyte
CL:0000182
T47D
CS57813
James Malone
CS57813 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158837&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158837&type=germplasm
GM12056
dorsal ectoderm anlage in statu nascendi
FBbt:00005832
test result
The recorded value of the outcome of some test.
skin cell
native skin
NCI Thesaurus: C12470
CS57854
James Malone
CS57854 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158878&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158878&type=germplasm
promyelocytic leukemia
CS57924
James Malone
CS57924 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005164920&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005164920&type=germplasm
neoplasia
James Malone
An abnormal tissue growth resulted from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant ones exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
NCI thesaurus http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C3262&bookmarktag=2 Date accessed: 30th October 2007
cleavage 4-cell
ZFS:0000003
light
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
CS57740
James Malone
CS57740 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158764&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158764&type=germplasm
invasive ductal carcinoma
infiltrating ductal carcinoma
DOID:6583
NCI Thesaurus: C4194
acinar cell carcinoma
DOID:3025
organism status
Use PATO qualities , e.g. dead
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. e.g. alive or dead
uninfected
NCI Thesaurus: C14165
A normal class is a special type of disease factor used as a control, that is, one which is not known to be affected by any disease; being approximately average or within certain limits; conforming with or constituting a norm or standard or level or type or social norm.
control
normal
James Malone
reference sample
sarcoma
James Malone
Type of cancer of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue.
DOID:1115
hereditary spastic paraplegia
DOID:2476
CS57812
James Malone
CS57812 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?id=1005158836&type=germplasm
http://www.arabidopsis.org/servlets/TairObject?id=1005158836&type=germplasm
GM12057
dorsal ectoderm primordium
FBbt:00005527
relationship
has_part
has_quality
part_of
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
As for part_of, with the additional constraint that subject and object may be identical
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C integral_part_of C' if and only if: C part_of C' AND C' has_part C
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
As for part_of, with the additional constraint that subject and object are distinct
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
derived_from