The Arabidopsis Information Resource (TAIR)
Helen Parkinson
classified
CRISP Thesaurus Version 2.5.2.0
Disease Ontology mappings to DiseaseOntology3 revision 2
National Cancer Institute Thesaurus mappings to version December 2007 (07.12e)
$version 1.0$
Foundational Model of Anatomy version date Fri Sep 15 13:29:00 BST 2006
MAT version 3.0
The Jackson Lab
Tomasz Adamusiak
James Malone
Zebrafish Anatomy and Development ontology mappings version 1.14 October 24 2007
Cell Type ontology mappings to Revision 1.23
Drosophila Gross Anatomy ontology Revision 1.22 December 11 2007
Beas2B
James Malone
GM11992
James Malone
ZF4
James Malone
prednisolone
CHEBI:8378
parathyroid
MAT:0000082
James Malone
NIH3T3-L1
James Malone
Becker's muscular dystrophy
Benign pseudohypertrophic muscular dystrophy
DOID:9884
James Malone
hypertension
DOID:10763
James Malone
cell property
CD8+
An attribute of a cell e.g. CD8+
James Malone
HIV-1
HIV-1 seropositive
NCI Thesaurus: C14220
James Malone
AU565
James Malone
ZR751
James Malone
ponasterone A
CHEBI:28135
thyroid
MAT:0000081
James Malone
GM11993
James Malone
papillary cystadenocarcinoma
DOID:3110
James Malone
obsolete_B lymphocyte
Consolidated with B cell (EFO_0000101), use B cell class instead.
B-lymphocyte
CL:0000236
NCI Thesaurus: C12474
radicle
MAT:0000415
James Malone
hyperplasia
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
James Malone
sampling time
James Malone
cell line
A cell line is a cell factor which describes a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism. The cells of such a population share common characteristics.
Atwood et al (2000) OED of Biochemistry and Molecular Biology, Oxford University Press.
James Malone
PAC2
James Malone
ZR7530
James Malone
head and neck squamous cell carcinoma
DOID:5520
James Malone
immature B cell
CL:0000816
James Malone
pirinixic acid
CHEBI:32509
thymus
MAT:0000080
James Malone
GM11994
James Malone
NCI-H929
James Malone
overall survival
James Malone
cellular modification
RNAi
The act of alteration or modification of a cell e.g. RNAi
James Malone
hepatocellular carcinoma
HCC
hepatoma
NCI Thesaurus: C3099
James Malone
B cell
B lymphocyte
B-lymphocyte
CL:0000236
NCI Thesaurus:C12474
James Malone
pioglitazone
CHEBI:8228
BEAS-2B
James Malone
ZR75B
James Malone
GM11995
James Malone
osteosarcoma
DOID:3347
James Malone
NIH3T3
James Malone
cell type
epithelial, glial.
A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.
James Malone
Hodgkin's lymphoma
DOID:353
James Malone
CS57603
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
James Malone
hypertrophic cardiomyopathy
DOID:11984
James Malone
BY5251
James Malone
chitin
CHEBI:17029
CS57716
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
James Malone
obsolete_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
GM12003
James Malone
dorsomedial neurosecretory cell
FBbt:00004011
James Malone
phenobarbital
CHEBI:8069
female
CARO:0000028
PATO:0000383
James Malone
3T3-L1
James Malone
cerebellum
cerebellum peduncles
NCI Thesaurus: C12445
James Malone
urethra
MAT:0000121
James Malone
293TsiLL
James Malone
risk status
The probability that an event will occur generally with unfavorable outcome.
James Malone
skin cell
native skin
NCI Thesaurus: C12470
James Malone
CS57606
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
James Malone
cambium
MAT:0000223
James Malone
R28
James Malone
obsolete_continuant
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
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.
CS57715
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
James Malone
cardiovascular system
MAT:0000016
James Malone
GM12004
James Malone
dose
The total quantity or strength of a substance administered at one time.
James Malone
organism part
tissue, organ, system, sperm, blood or body location (arm).
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).
James Malone
chlorpromazine
CHEBI:3647
male
CARO:0000027
PATO:0000384
James Malone
pentamidine
CHEBI:45081
rheumatoid arthritis
DOID:7148
James Malone
293T
James Malone
CS57610
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
James Malone
central nervous system cancer
NCI Thesaurus: C4627
James Malone
R43
James Malone
ureter
MAT:0000120
James Malone
tuber
MAT:0000358
James Malone
skin disease
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
James Malone
fat tissue
MAT:0000015
James Malone
CS57714
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
James Malone
CS57719
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
James Malone
organism
Drosophila melanogaster
The genus and species (and subspecies) of the organism from which the biomaterial is derived from. E.g Drosophila melanogaster
James Malone
carbon monoxide
CHEBI:17245
A549
James Malone
hermaphrodite
An organism having both male and female sexual characteristics and organs.
NCI Thesaurus: C45909
PATO:0001340
James Malone
lateral shoot meristem
MAT:0000225
James Malone
PC12
James Malone
CS57615
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
James Malone
sampling site
James Malone
cerebrospinal fluid
NCI Thesaurus: C12692
James Malone
TBP-71Q-16
TBP-71Q-16 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/008216.html
JAX:008216
James Malone
digestive system component
MAT:0000018
James Malone
Duchenne muscular dystrophy
DOID:11723
James Malone
mating type
A mating type is a biomaterial factor which describes the type of sexual reproduction through isogamy occur in eukaryotes that undergo.
James Malone
CS57717
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
James Malone
celecoxib
CHEBI:41423
operator variation
The effects of different investigators, laboratories, or organizations on experimental results are studied.
600MPE
James Malone
R18
James Malone
apical shoot meristem
MAT:0000224
James Malone
CB6F1
CB6F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100007.html
JAX:100007
James Malone
cerebral cortex
brain cortex
MAT:0000108
NCI Thesaurus: C12443
James Malone
CS57616
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
James Malone
obsolete_sample factor
synonym with material entity
craniofacial tissue
MAT:0000017
James Malone
renal clear cell carcinoma
DOID:4467
James Malone
exercise
Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness.
James Malone
animal developmental tissue
MAT:0000019
James Malone
sulindac
CHEBI:9352
liver carcinoma
James Malone
CBA/CaJ
CBA/CaJ is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000654.html
JAX:000654
James Malone
chondrocyte
CL:0000138
James Malone
alpha-D-glucose
CHEBI:17925
somatic cell
NCI Thesaurus: C12949
James Malone
congenital bilateral absence of the vas deferens
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
James Malone
trachea
MAT:0000137
James Malone
CS57727
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
James Malone
obsolete class
obsolete_experiment type
This is no longer needed - use process or study design (if the design is for study).
ChIP-Chip array
An experiment type is an experimental factor describing the area of technology that was used to perform an experiment.
renal cell carcinoma
DOID:4450
James Malone
liver heptocellular carcinoma
James Malone
sulforaphane
CHEBI:47807
lung
MAT:0000135
James Malone
BDC2.5/NOD
BDC2.5/NOD is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/004460.html
JAX:004460
James Malone
spindle cell tumor
DOID:2414
James Malone
all-trans-retinoic acid
CHEBI:15367
osteoblast
CL:0000062
James Malone
obsolete_compound factor
use synonym chemical compound
CS57722
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
James Malone
obsolete_experimental design
obsolete - synonym with experiment type
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.
respiratory system disease
DOID:1579
James Malone
obsolete_CNS brain striatum MMHCC
Use corpus striatum instead (EFO_0000381)
NCI Thesaurus: C22622
small cell lung carcinoma
DOID:5409
James Malone
ileum
MAT:0000282
NCI Thesaurus:C12387
James Malone
gland
exocrine system
MAT:0000021
James Malone
gill
MAT:0000134
James Malone
R46
James Malone
CS57859
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
James Malone
all-cis-docosa-4,7,10,13,16,19-hexaenoic acid
CHEBI:28125
synovial sarcoma
DOID:5485
NCI Thesaurus:C3400
James Malone
congestive heart failure
DOID:395
James Malone
CS57732
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
James Malone
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.
James Malone
anterior endoderm anlage in statu nascendi
FBbt:00005418
James Malone
olfactory lobe
olfactory bulb
MAT:0000116
NCI Thesaurus: C22619
James Malone
behavioural disease
A bacterial disease is a disease factor that is caused primarily by bacteria.
behavioral disease
DOID:150
James Malone
smooth muscle cell
primary aortic smooth muscle cell
primary uterine smooth muscle cell
CL:0000192
James Malone
animal fluid
MAT:0000020
James Malone
bronchus
MAT:0000133
James Malone
sulphur dioxide
CHEBI:18422
CS57867
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
James Malone
congestive cardiomyopathy
DOID:12930
James Malone
CS57731
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
James Malone
exposure
exposure to cigarette smoke
The act of subjecting someone or something to an influencing experience. E.g. exposure to cigarette smoke
James Malone
obsolete_infiltrating ductal carcinoma
Made obsolete: considered as synonym to invasive ductal carcinoma
appendage
MAT:0000023
James Malone
hypothalamus
MAT:0000112
NCI Thesaurus: C22616
James Malone
129S1/SvImJ
http://jaxmice.jax.org/strain/002248.html
James Malone
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
James Malone
anterior endoderm primordium
FBbt:00005524
James Malone
hermaphrodite gonad
MAT:0000165
James Malone
sensillum
MAT:0000163
James Malone
CS57854
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
James Malone
intervertebral disc
FMA:10446
MA:0000110
James Malone
antipsychotic drug
CHEBI:35476
steroid hormone
CHEBI:26764
squamous cell lung carcinoma
DOID:3907
James Malone
external control ratio
Use of spiked in controls in a measurement of the spiked in external/internal ratio
haemopoietic system
hematological system
MAT:0000022
James Malone
obsolete_infiltrating lobular carcinoma
Made obsolete: considered as synonym to invasive lobular carcinoma
jejunum
MAT:0000045
NCI Thesaurus:C12388
James Malone
ChIP-Chip
An experiment where chromatin immunoprecipitation (ChIP) is used in combination with microarray technology.
<WEB> http://en.wikipedia.org/wiki/ChIP-on-chip
James Malone
obsolete_CNS brain hippocampus MMHCC
Obsolete - term hippocampus already exists
NCI Thesaurus: C22615
anterior midgut primordium
FBbt:00000444
James Malone
CS57733
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
James Malone
male reproductive system
male genital system
MAT:0000029
James Malone
staurosporine
CHEBI:15738
stem cell
adipose tissue-derived stem cell
conditioned mesenchymal stem cell
mesenchymal stem cell
CL:0000034
James Malone
CS57858
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
James Malone
vertebra
FMA:9914
MA:0000309
James Malone
antibiotic
CHEBI:22582
sensory bristle
MAT:0000152
James Malone
invasive ductal carcinoma
infiltrating ductal carcinoma
DOID:6583
NCI Thesaurus: C4194
James Malone
extra-adrenal sympathetic paraganglioma
NCI Thesaurus: C48576
James Malone
CNS brain cerebellum MMHCC
NCI Thesaurus: C22609
James Malone
C57BL/6J
A/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000664.html
C57BL6
JAX:000664
James Malone
cell factor
James Malone
anterior spiracle specific anlage
FBbt:00005487
James Malone
regulatory T-cell
pancreatic T regulatory cell
CL:0000815
James Malone
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
James Malone
CS57848
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
James Malone
androgen
CHEBI:50113
diaphragm
MAT:0000502
James Malone
sucrose
CHEBI:17992
neonate
newborn
NCI Thesaurus:C16731
James Malone
spondyloarthropathy
DOID:1123
James Malone
Kaposi's sarcoma cell
NCI Thesaurus: C9087
James Malone
Brown-Norway
Brown-Norway is a rat strain as described in http://www.informatics.jax.org/external/festing/rat/docs/BN.shtml
BN
http://www.informatics.jax.org/external/festing/rat/docs/BN.shtml
James Malone
antibody
An antibody function (or antigen binding function) is an infection-fighting protein molecule in blood or secretory fluids that tags, neutralizes, and helps destroy pathogenic microorganisms such as bacteria, viruses and toxins.
James Malone
obsolete_caudate nucleus
Duplicated term, use EFO_0000907
NCI Thesaurus: C12451
129P1/ReJ
http://jaxmice.jax.org/strain/001137.html
James Malone
proteomic profiling
Antibody profiling experiment
An experiment where proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling
ArrayExpress production team
James Malone
CS57850
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
James Malone
WI38
James Malone
precentral gyrus
FMA:61894
NCI Thesaurus:C33393
James Malone
spiracle
MAT:0000208
James Malone
streptozotocin
CHEBI:9288
amitriptyline
CHEBI:2666
squamous cell carcinoma
squamous cell cancer
DOID:1749
James Malone
tamoxifen
CHEBI:41774
skin
MAT:0000284
James Malone
coronary artery disease
DOID:3363
James Malone
acute quadriplegic myopathy
NCI Metathesaurus: C1406910
James Malone
arachidonic acid
CHEBI:15843
CS57847
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
James Malone
metabolism disease
DOID:0014667
James Malone
GM12892
James Malone
aortic stenosis
DOID:1712
James Malone
imatinib
CHEBI:45783
bacterial disease
A bacterial disease is a disease factor that is caused primarily by bacteria.
James Malone
taxol
CHEBI:45863
tail
MAT:0000094
James Malone
adaxial cells
ZFA:0000003
James Malone
corpus allatum
FBbt:00001716
MAT:0000210
James Malone
mesothelioma
DOID:2645
James Malone
CS57843
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
James Malone
aorta
MAT:0000035
NCI Thesaurus: C12669
James Malone
H209
James Malone
Eukaryota
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_2759
James Malone
hydroxyurea
CHEBI:44423
tetraethylenepentamine
CHEBI:49798
ductal adenocarcinoma
DOID:3008
James Malone
antirheumatic drug
CHEBI:35842
adductor mandibulae complex
ZFA:0000311
James Malone
scale
MAT:0000257
James Malone
CS57842
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
James Malone
H720
James Malone
hydrogen peroxide
CHEBI:16240
Bacteria
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_2
James Malone
apoptotic amnioserosa
FBbt:00005556
James Malone
thiopurines
CHEBI:35666
adenocarcinoma
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
James Malone
apratoxin A
CHEBI:35212
CS57840
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
James Malone
adult segment
MAT:0000271
James Malone
HBL100
James Malone
Hexadecanoic acid
CHEBI:15756
Archaea
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_2157
James Malone
apical meristem
PO:0020148
James Malone
endocrine system disease
DOID:28
James Malone
trunk
MAT:0000296
James Malone
adenohypophyseal placode
ZFA:0001198
James Malone
metabolomic profiling
An experiment in which one or more metabolites are analysed.
metabolimic profiling
ArrayExpress production team
James Malone
conjunctiva
NCI Thesaurus: C12341
James Malone
HC toxin
CHEBI:48028
HCC1007
James Malone
event death
An event that has caused the permanent cessation of all vital functions; the end of life. Can be applied to a whole organism or to a part of an organism.
James Malone
multiple myeloma
DOID:9538
James Malone
neck
MAT:0000297
James Malone
microRNA profiling
An experiment in which a microRNA array is used to analyse the microRNA component of the transcriptome.
ArrayExpress production team
James Malone
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.
James Malone
HCC1143
James Malone
array design
Descriptions pertaining to the design of the array.
James Malone
halothane
CHEBI:5615
head
MAT:0000294
James Malone
conventional clear cell renal carcinoma
DOID:4467
James Malone
genotyping
An experiment in which variation in the genome is analysed
ArrayExpress production team
James Malone
event free survival time
James Malone
salivary gland
MAT:0000079
James Malone
methylation profiling
An experiment in which the methylation state is determined and is compared between samples.
Methylation specific oligonucleotide microarray
ArrayExpress production team
James Malone
thorax
MAT:0000295
James Malone
cornea
NCI Thesaurus: C12342
James Malone
surfactants
CHEBI:35195
ganglion
MAT:0000343
James Malone
event distant metastases
Occurrence of a metastasis measured from some defined time point
James Malone
protocol
A protocol is an information entity which is a set of instructions that describe an how an experiment is done.
plan specification
James Malone
CS57619
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
James Malone
immune system disease
DOID:2914
James Malone
taproot
MAT:0000222
James Malone
BJABK3
James Malone
cardiomyopathy
DOID:3978
James Malone
medullary thymic epithelial cell
NCI Thesaurus: C45702
James Malone
plant embryo
MAT:0000226
James Malone
pathogen
A biological agent that causes disease or illness to its host
James Malone
pituitary
MAT:0000077
James Malone
function
A function is an entity which is an essentially end-directed activity of a material entity in virtue of that entity being a specific kind of entity in the kind or kinds of contexts that it is made for. For example,
Derived from BFO:function
James Malone
prostate
MAT:0000078
James Malone
immunoprecipitate
The antibody used to precipitate an antigen out of a solution during the process of immunoprecipitation.
James Malone
root hair
MAT:0000352
James Malone
CS57618
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
James Malone
BL41K3
James Malone
cardiovascular disease
DOID:1287
James Malone
medullary breast carcinoma
DOID:5605
James Malone
mating type h minus
MO_407
James Malone
ectoderm anlage in statu nascendi
FBbt:00005414
James Malone
pathogen test
Not sure what this class represents - possibly redundant
Tests and results for pathogens infecting organism from which the biosource is derived
root nodule
MAT:0000353
James Malone
abdomen
MAT:0000298
James Malone
role
For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
Derived from BFO:role
James Malone
CS57621
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
James Malone
BT20
James Malone
obsolete_individual
is equivalent to an instance of class organism
Identifier or name of the individual organism from which the biomaterial was derived.
megakaryocyte progenitor cell
CL:0000553
James Malone
pancreas
MAT:0000075
James Malone
papillary thyroid carcinoma
DOID:3969
James Malone
embryonic anal pad
FBbt:00005748
James Malone
root cap
MAT:0000357
James Malone
female reproductive system
female genital system
MAT:0000028
James Malone
CS57620
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
James Malone
BT474
James Malone
obsolete_individual genetic characteristic
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
acute lymphocytic leukemia
ALL
DOID:9952
James Malone
megakaryocyte
CL:0000556
James Malone
islet of Langerhans
James Malone
parietal cell
CL:0000162
James Malone
embryonal rhabdomyosarcoma
DOID:3246
James Malone
isoflurane
CHEBI:6015
unit
Import from unit ontology
James Malone
infection
The state of being infected such as from the introduction of a foreign agent such as serum, vaccine, antigenic substance or organism.
James Malone
MOLT-4
James Malone
gall bladder
MAT:0000072
James Malone
progesterone
CHEBI:17026
ductal carcinoma in situ
DOID:8791
carcinoma in situ of breast
James Malone
mesangial phagocyte
mesangial cell
CL:0000777
James Malone
acute monoblastic leukaemia
DOID:8864
James Malone
GM11839
James Malone
isoflavone
CHEBI:18220
data set
A data set is an information entity that is an aggregate of other information entities that have something in common and are considered to form a unit.
James Malone
infertility
sterile
DOID:5223
James Malone
CS57622
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
James Malone
GM12874
James Malone
GM12873
James Malone
propofol
CHEBI:44915
mammary gland
MAT:0000073
James Malone
ductal breast carcinoma
DOID:3008
James Malone
GM11832
James Malone
meningitis
DOID:9471
James Malone
papillary renal cell carcinoma
DOID:4465
James Malone
acute myeloid leukemia
AML
DOID:9119
James Malone
measurement
A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
James Malone
indomethacin
CHEBI:49662
injury
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity
James Malone
GM12875
James Malone
ecotype
the A. thaliana Ecotype Ler
A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
James Malone
mesodermal cell
CL:0000222
James Malone
duodenum
MAT:0000044
James Malone
acute myelomonocytic leukemia
AMML
Acute M4 Myeloid Leukemia
NCI Thesaurus: C7463
James Malone
GM11882
James Malone
pregnenolone 16alpha-carbonitrile
CHEBI:35591
indole-3-acetic acid
CHEBI:16411
inner cell mass
NCI Thesaurus: C13740
James Malone
GM12891
James Malone
material property
An entity property is an entity which is a property or characteristic of some other entity. For example, the material mouse has the colour white.
Derived from BFO:function
James Malone
lateral root meristem
MAT:0000221
James Malone
mesenchymal stem cell
conditioned mesenchymal stem cell
NCI Thesaurus: C43423
James Malone
duration
James Malone
adrenal medulla
MAT:0000495
James Malone
acute promyelocytic leukemia
APML
NCI Thesaurus: C3182
James Malone
GM11881
James Malone
prochlorperazine
CHEBI:8435
obsolete_nucleic acid extracted
Not needed.
The type of nucleic acid obtained as a result of following a given protocol.
GM12146
James Malone
gastrula 50%-epiboly
ZFS:0000017
James Malone
TERV-ST
James Malone
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
James Malone
non ionic surfactant
CHEBI:38828
obsolete_malignant peripheral nerve sheath tumor class
DOID:5940
CS57625
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
James Malone
chronic gastritis
DOID:4032
James Malone
CS57776
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
James Malone
CS57737
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
James Malone
972h-
972h- is a yeast strain as described in article PMID 12753
PMID: 12753
James Malone
GM12154
James Malone
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
James Malone
cleavage stage
James Malone
TERV-ST110
James Malone
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
James Malone
nocodazole
CHEBI:34892
rat strain
Strain or line specific to rat.
James Malone
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.
CS57626
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
James Malone
metabolic syndrome
James Malone
CS57771
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
James Malone
CS57735
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
James Malone
obsolete_white blood cell
use leukocyte EFO_0000566
CL:0000738
James Malone
obsolete_independent continuant
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
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.
clozapine
CHEBI:3766
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
An experimental factor in Array Express.
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
Helen Parkinson
James Malone
GM12144
James Malone
caecum
MAT:0000288
James Malone
MALT lymphoma
James Malone
novobiocin
CHEBI:28368
Pseudomonas infection
DOID:2903
James Malone
essential thrombocythemia
hemorrhagic thrombocythemia
DOID:2224
James Malone
insulinoma
DOID:3903
James Malone
chromophobe renal cell carcinoma
DOID:4471
James Malone
pterygium
DOID:10526
James Malone
nutrient
this should become a quality of a material i think
chow, fertilizer, DEMM 10%FBS
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
James Malone
MDAMB361
James Malone
CS57778
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
James Malone
CS57511
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
James Malone
cobalt dichloride
CHEBI:35696
GM12145
James Malone
non-steroidal anti-inflammatory drug
CHEBI:35475
MELAS syndrome
DOID:3687
James Malone
ovarian carcinoma
James Malone
TERV-AntiSenseB56
James Malone
psychiatric disorder
A major affective disorder marked by severe mood swings (manic or major depressive episodes) and a tendency to remission and recurrence.
NCI Metathesaurus: C34423
James Malone
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
James Malone
instrument
To be imported from OBI
James Malone
CS57624
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
James Malone
chordoma
DOID:3302
James Malone
number of injections
The scalar number of injections administered to a material or organism.
James Malone
MDAMB415
James Malone
invertebrate ganglion
MAT:0000207
James Malone
CS57777
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
James Malone
CS57512
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
James Malone
morbid obesity
DOID:11981
James Malone
U373
James Malone
microglial cell
mixed glial cells (predominantly microglia)
CL:0000129
James Malone
CS57751
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
James Malone
neurofibroma
DOID:962
James Malone
colchicine
CHEBI:23359
dorsal root ganglion
spinal ganglion
MAT:0000162
James Malone
Pectobacterium carotovorum infection
Erwinia carotovora infection
NCI Metathesaurus: C0085485
James Malone
gastrula stage
MAT:0000063
James Malone
SALK_049497
SALK_049497 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=germplasm&id=4652085
Germplasm:4652085
James Malone
MDAMB435
Was originally considered to be a breast cancer cell line but has since been identified as a melanoma cell line.
James Malone
lateral line system
MAT:0000249
James Malone
psoriasis
DOID:8893
James Malone
CS57629
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
James Malone
obesity
DOID:9970
James Malone
CS57515
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
James Malone
lymphoblastic leukemia MOLT-4
James Malone
U87
James Malone
mitochondrial disorder
hyperglycaemia
DOID:700
James Malone
CS57750
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
James Malone
copper(2+) sulfate
CHEBI:23414
body ganglion
trunk ganglion
MAT:0000344
James Malone
neuroblastoma
DOID:769
James Malone
gastrula germ-ring
ZFS:0000018
James Malone
Enterococcus faecalis infection
NCI Metathesaurus: C0038404
James Malone
chordotonal organ
MAT:0000209
James Malone
inflorescence
MAT:0000233
James Malone
MDAMB436
James Malone
CS57630
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
James Malone
A/J
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
James Malone
memory impairment
NCI Metathesuarus: C55427
James Malone
obsolete_protocol factor
synonymous with protocol
A protocol factor is an experimental factor which describes factors that describe the protocol design of an experiment.
James Malone
THP-1
James Malone
CS57520
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
James Malone
genetic trait
Genetic traits are small inherited parts of the phenotype of an organism
James Malone
creatine
CHEBI:16919
CS57743
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
James Malone
embryonic antennal sense organ
FBbt:00005568
James Malone
neuronal stem cell
neural stem progenitor cell
CL:0000047
James Malone
gastrula bud
ZFS:0000022
James Malone
cranial ganglion
cranial ganglia
head ganglion
James Malone
craniofacial skeleton bone
MAT:0000149
James Malone
CS57770
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
James Malone
CS57627
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
James Malone
obsolete_protocol
Merged plan specification and protocol and made synonymous hence this class is redundant.
B6.Cg-Tg(SOD1-G93A)1Gur/J
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
James Malone
chronic myelogenous leukemia
CML
DOID:8552
James Malone
lung carcinoma
DOID:3905
James Malone
fruit
MAT:0000232
James Malone
MDAMB453
James Malone
U266
James Malone
CS57521
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
James Malone
gastrula 75%-epiboly
ZFS:0000020
James Malone
genetic modification
Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection
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.
neuron
primary cortex neuron
CL:0000540
James Malone
CS57742
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
James Malone
cyfluthrin
CHEBI:4034
CS57740
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
James Malone
trigeminal ganglion
MAT:0000511
James Malone
prostate adenocarcinoma
prostate cancer
DOID:2526
James Malone
gastrula 90%-epiboly
ZFS:0000021
James Malone
sapphyrin
CHEBI:36779
spinal cord
MAT:0000183
James Malone
CS57628
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
James Malone
C3H/HeJ
C3H/HeJ is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000659.html
JAX:000659
James Malone
chronic granulomatous disease
DOID:3265
James Malone
folate deficiency
folic acid deficiency
DOID:8453
James Malone
axial skeleton
MAT:0000148
James Malone
tepal
MAT:0000356
James Malone
MDAMB468
James Malone
enteric nervous system
enteric PNS
MAT:0000102
James Malone
limb bone
limb skeleton
MAT:0000151
James Malone
salicylic acid
CHEBI:16914
prognostic subgroup
This needs to be a defined class. It is a population specifically defined by the probability of some outcome.
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
epigenetic status
Loss of imprinting occurs in some tumour cells
Epigenetic status describes the imprinting state of a sample. E.g. Loss of imprinting occurs in some tumour cells
fertilized egg stage
zygote
MAT:0000074
ZFS:0000001
James Malone
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
James Malone
corneal limbus
corneoscleral limbus
FMA:58342
NCI Thesaurus: C12823
James Malone
colon
MAP:0000001
NCI Thesaurus: C12382
James Malone
organ of corti
NCI Thesaurus: C33223
James Malone
CS57537
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
James Malone
ventral nerve cord
MAT:0000339
James Malone
fetus
embryo late (growth) stage
MAT:0000399
James Malone
S-[2,3-bis(palmitoyloxy)propyl]-Cys-Ser-Lys-Lys-Lys-Lys
CHEBI:46889
Met5A
James Malone
exoskeleton
MAT:0000150
James Malone
progeria syndrome
DOID:3911
James Malone
epilepsy
DOID:1826
James Malone
hatching pec-fin
ZFS:0000034
James Malone
seminiferous tubules
NCI Thesaurus:C13047
James Malone
undifferentiated sarcoma
DOID:6191
James Malone
CS57758
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
James Malone
cololrectal tumor
James Malone
age-related macular degeneration
DOID:10871
James Malone
CS57541
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
James Malone
MM1
James Malone
rotenone
CHEBI:28201
pharyngeal nervous system
MAT:0000341
James Malone
Drosophila melanogaster strain
Strain or line specific to Drosophila melanogaster
James Malone
epiblast cell
epiblast stem cell
primary lymphatic endothelial cell
CL:0000352
James Malone
hatching stage
ZFS:0000033
James Malone
primordial germ cell
CL:0000670
James Malone
myositis
inflammatory myopathy
DOID:633
James Malone
CS57753
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
James Malone
back
FMA:14181
NCI Thesaurus: C13062
James Malone
virus strain
Strain or line specific to virus
James Malone
2,3,7,8-tetrachlorodibenzodioxine
CHEBI:28119
CS57543
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
James Malone
pelvic girdle
MAT:0000182
James Malone
pulmonary arterial hypertension
NCI Thesaurus:C3120
James Malone
somatic nervous system
MAT:0000342
James Malone
Canton S
Canton-S
FBst0000001Â
James Malone
gastrula shield
ZFS:0000019
James Malone
epigenetic factor
Hibiscus chlorotic ringspot virus
NCI Metathesaurus: C1017212
James Malone
T cell acute lymphoblastic leukemia
DOID:5603
James Malone
CS57752
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
James Malone
vehicle
A carrier or inert medium used as a solvent (or diluent) in which some compound is formulated and or administered.
James Malone
extraembryonic tissue
MAT:0000061
James Malone
inner ear
MIAA:0000145
James Malone
pectoral girdle
MAT:0000181
James Malone
rosiglitazone
CHEBI:50122
amnioserosa anlage in statu nascendi
FBbt:00005422
James Malone
CS57783
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
James Malone
peripheral nervous system
PNS
MAT:0000338
James Malone
plant component
MAT:0000003
James Malone
chondrosarcoma
DOID:3371
James Malone
myelodysplastic syndrome
James Malone
erythrocyte
CL:0000232
James Malone
type II diabetes mellitus
diabetes mellitus type 2
DOID:9351
James Malone
cartilage
MAT:0000189
James Malone
rofecoxib
CHEBI:8887
4-hydroxy-2-nonenal
CHEBI:32585
washing
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.
James Malone
CS57883
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
James Malone
CS57779
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
James Malone
observation
The act of regarding attentively and studying facts and occurrences, gathering data through analyzing, measuring, and drawing conclusions
James Malone
somatic nervous system
somatic PNS
MAT:0000099
James Malone
chondromyxoid fibroma
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
James Malone
amygdala
amygdala central nucleus
MAT:0000289
NCI Thesaurus: C12440
James Malone
fungal component
MAT:0000002
James Malone
oral squamous cell carcinoma
James Malone
esophageal adenocarcinoma
DOID:4914
James Malone
retinoic acid
CHEBI:26536
pulmonary hypertension
DOID:6432
James Malone
joint
MAT:0000188
James Malone
CS57884
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
James Malone
3',5'-cyclic AMP
CHEBI:17489
vitamin B12 deficiency
DOID:8459
James Malone
scapula
shoulder blade
NCI Thesaurus: C12783
James Malone
sympathetic nervous system
sympathetic PNS
MAT:0000100
James Malone
segmentation 20-25 somites
ZFS:0000027
James Malone
chondroblastoma
DOID:2649
James Malone
CS57789
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
James Malone
well-differentiated_sarcoma
James Malone
epithelial cell
epithelial
medullary thymic epithelial cell
oesophageal cell
CL:0000066
James Malone
animal component
MAT:0000001
James Malone
metastatic prostate cancer
James Malone
CS57886
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
James Malone
5-fluorouracil
CHEBI:46345
rapamycin
CHEBI:9168
tonsil
NCI Thesaurus: C12802
James Malone
segmentation 26+ somites
ZFS:0000028
James Malone
childhood acute myeloid leukemia
NIC Thesaurus: C9160
James Malone
CS57785
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
James Malone
amnioserosa
FBbt:00000095
James Malone
bronchoalveolar lavage cell
alveolar epithelial type I
bronchial epithelial cells
epithelial cell of lung
James Malone
CL:0000082
alveolar epithelial type II
bronchial epithelial
mucoid ductal carcinoma
James Malone
anatomy basic component
MAT:0000000
James Malone
parasympathetic nervous system
parasympathetic PNS
MAT:0000101
James Malone
Rett syndrome
Rett disorder
DOID:1206
James Malone
raloxifene
CHEBI:8772
CS57890
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
James Malone
5-aza-2'-deoxycytidine
CHEBI:50131
trigeminal nerve
NCI Thesaurus: C12806
James Malone
well-differentiated_liposarcoma
James Malone
CS57874
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
James Malone
chemical compound
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
James Malone
obsolete_accumbens nucleus
duplicated use class EFO_0000906
NCI Thesaurus: C52733
sodium chloride
CHEBI:26710
embryonic central brain glia
FBbt:00005663
James Malone
bladder tumor
DOID:5428
James Malone
6alpha-methylprednisolone
CHEBI:6888
diabetic nephropathy
DOID:2370
James Malone
quality
A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
Derived from BFO:quality
James Malone
anlage in statu nascendi
FBbt:00005413
James Malone
HCC2185
James Malone
genetic disorder
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
James Malone
gefitinib
CHEBI:49668
acinar cell carcinoma
DOID:3025
James Malone
CS57873
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
James Malone
compound based treatment
James Malone
sodium pyruvate
CHEBI:50144
AACOCF3
CHEBI:2341
embryonic central brain
FBbt:00005662
James Malone
bladder mucosa
NCI Thesaurus: C32205
James Malone
information entity
An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set.
James Malone
diffuse gastric adenocarcinoma
NCI Thesaurus: C9159
James Malone
angioimmunoblastic T-cell lymphoma
NCI Thesaurus: C7528
James Malone
genetic factor
everything under here....
HCC3153
James Malone
fulvestrant
CHEBI:31638
median fin skeleton
MAT:0000277
James Malone
abdominal cavity
NCI Thesaurus: C12664
James Malone
columnar neuron
intermediolateral column motoneuron
CL:0000112
James Malone
abscisic acid
CHEBI:22152
CS57876
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
James Malone
embryonic brain
FBbt:00001060
James Malone
James Malone
NCI Thesaurus: C12434
blood
blood cells
peripheral blood
MAT:0000083
whole blood
peripheral blood progenitor
disposition
For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
A disposition is an entity that essentially causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
Derived from BFO:disposition
James Malone
anthrax
DOID:7427
James Malone
glucitol
CHEBI:30911
anal pad specific anlage
FBbt:00005482
James Malone
HCC202
James Malone
paired fin skeleton
MAT:0000278
James Malone
common variable immunodeficiency
CVID
DOID:12177
James Malone
abdominal skin
NCI Thesaurus: C52758
James Malone
actinomycin D
CHEBI:27666
CS57875
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
James Malone
blastocyst
NCI Thesaurus: C13739
James Malone
selenium
CHEBI:27568
site
A site is an entity which consists of a characteristic spatial shape in relation to some arrangement of other material entities.
Derived from BFO:site
James Malone
Drosophila C virus
NCI Metathesaurus: C0318594
James Malone
diabetes mellitus
DOID:9351
James Malone
genistein
CHEBI:28088
HCC2157
James Malone
amyotrophic lateral sclerosis
DOID:332
James Malone
colon mucinous adenocarcinoma
DOID:3029
James Malone
bone
MAT:0000299
NCI Thesaurus: C12366
James Malone
aldosterone
CHEBI:27584
acute lymphoblastic leukemia
ALL
DOID:5600
James Malone
vertebral column
backbone
spine
MAT:0000148
James Malone
connective tissue
fascia
tendon
MAT:0000301
James Malone
environmental stress
change in temperature, change in watering regime
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
James Malone
interneuron
GABAergic interneuron
CL:0000099
James Malone
anal region
anus
MAT:0000042
James Malone
skeletal muscle
MAT:0000302
James Malone
colorectal adenocarcinoma
colorectal cancer
DOID:9256
James Malone
blood vessel endothelial cell
primary blood vessel endothelial cell
primary microvascular endothelial cell
umbilical vein endothelial cell
CL:0000071
James Malone
dermis
MAT:0000153
James Malone
intercostal muscle
FMA:13354
NCI:C32824
James Malone
intracranial hemorrhage NOS
DOID:1126
James Malone
rectum
MAT:0000050
James Malone
liver
MAT:0000097
James Malone
anterior endoderm anlage
FBbt:00000210
James Malone
_problematic
Concepts that are not well defined or are difficult to place
colon adenocarcinoma
DOID:234
James Malone
embryo
embryo early (growth) stage
NCI:C28147
James Malone
CS57871
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
James Malone
epidermis
MAT:0000154
James Malone
active gastritis
DOID:4029
James Malone
yeast strain
Strain or line specific to yeast
James Malone
appendix
MAT:0000287
James Malone
antennal primordium2
FBbt:00005537
James Malone
dentate gyrus
MAT:0000114
NCI Thesaurus: C22615
James Malone
colon carcinoma
DOID:1520
James Malone
bone MMHCC
NCI Thesaurus: C22682
James Malone
CS57870
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
James Malone
feather
MAT:0000156
James Malone
acute erythroid leukemia
DOID:1239
James Malone
antennal primordium1
FBbt:00005510
James Malone
smooth muscle
MAT:0000303
James Malone
267B1
James Malone
storage organ
MAT:0000366
James Malone
irradiate
The process of treating a material with radiation
James Malone
haloperidol
CHEBI:5613
petal
MAT:0000354
James Malone
globus pallidus
MAT:0000510
James Malone
ascending colon
MAT:0000311
James Malone
nail
claw
MAT:0000158
James Malone
oxamic acid
CHEBI:18058
ganglioneuroma
NCI Thesaurus:C3049
James Malone
chromium
CHEBI:28073
monophasic synovial sarcoma
DOID:5495
James Malone
GM12006
James Malone
irritable bowel syndrome
DOID:9778
James Malone
267B1 Ki-ras
James Malone
sepal
MAT:0000355
James Malone
growth hormone
CHEBI:37845
vascular tissue
MAT:0000362
James Malone
CS57641
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
James Malone
pigment
pigmentation
MAT:0000159
James Malone
basal ganglion
MAT:0000450
James Malone
paracetamol
CHEBI:46195
HCC1187
James Malone
oligoastrocytoma
DOID:7912
James Malone
follicular thyroid carcinoma
follicular carcinoma
DOID:3962
James Malone
transverse colon
MAT:0000312
James Malone
embryonic corpus cardiacum
FBbt:00001720
James Malone
UBOC1
James Malone
chlorpyrifos
CHEBI:34631
GM12005
James Malone
mononuclear cell
CL:0000842
James Malone
plant developmental tissue
MAT:0000518
James Malone
invasive ductal and lobular carcinoma
DOID:6583
James Malone
CS57637
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
James Malone
population based study
NCI Thesaurus:C15716
James Malone
Tomasz Adamusiak
hair
vibrissa
MAT:0000160
James Malone
cisplatin
CHEBI:27899
caudate nucleus
MAT:0000513
NCI Thesaurus: C12451
James Malone
bud
MAT:0000229
James Malone
UACC812
James Malone
embryonic corpus allatum
FBbt:00001719
James Malone
ganglioneuroblastoma
DOID:4163
James Malone
descending colon
MAT:0000313
James Malone
oligoastroglioma
DOID:7912
James Malone
monocyte
naive
CL:0000576
James Malone
invasive lobular carcinoma
infiltrating lobular carcinoma
DOID:3460
James Malone
plant reproductive system
MAT:0000514
James Malone
CS57631
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
James Malone
pharyngeal arch
MAT:0000242
James Malone
flower
MAT:0000231
James Malone
NCI Thesaurus: C52733
accumbens nucleus
nucleus accumbens shell
James Malone
nucleus accumbens core
MAT:0000512
nucleus accumbens whole
ciclosporin A
CHEBI:4031
gastric adenocarcinoma
DOID:3717
James Malone
embryonic central nervous system
FBbt:00001056
James Malone
U937
James Malone
sigmoid colon
MAT:0000314
James Malone
oligodendroglioma
DOID:3181
James Malone
mixed lobular and ductal breast carcinoma
DOID:6582
James Malone
forebrain
MAT:0000105
James Malone
clotrimazole
CHEBI:3764
race
NCI Thesaurus:C17049
James Malone
seed coat
MAT:0000228
James Malone
HCC1937
James Malone
glucose
CHEBI:17234
kaposi's sarcoma
DOID:8632
James Malone
unspecified peripheral T-cell lymphoma
James Malone
GM12057
James Malone
ochratoxin A
CHEBI:7719
129/Sv
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
James Malone
embryonic central brain surface glia
FBbt:00005664
James Malone
gastric intestinal type adenocarcinoma
DOID:8026
James Malone
cotyledon
MAT:0000359
James Malone
central nervous system
neuraxis
MAT:0000457
James Malone
clofibrate
CHEBI:3750
HCC1954
James Malone
twin study
A twin study is a study design in behavior genetics which aid the study of individual differences between genetically identical twins by highlighting the role of environmental and genetic causes on behavior.
Wikipedia definition, modified by editor.
James Malone
Tomasz Adamusiak
glucosamine
CHEBI:5417
keratinizing squamous cell carcinoma
DOID:5521
James Malone
GM12056
James Malone
oligomycin A
CHEBI:28285
embryonic central brain pars intercerebralis
FBbt:00005667
James Malone
129S6
129S6 is a substrain of the mouse strain 129 as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
129S6/SvEvTac
http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
James Malone
Wilms' tumor
nephroblastoma
DOID:2414
James Malone
large intestine
hindgut
MAT:0000046
James Malone
gastrointestinal stromal tumor
DOID:9253
James Malone
HCC1500
James Malone
gene knock out
glutathione
CHEBI:16856
obsolete_pretreatment
bladder MMHCC
NCI Thesaurus: C22729
James Malone
ischaemia
ischaemia
DOID:326
James Malone
material entity
A heart, a human, a fly, a microarray.
A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
sample factor
Dervied from BFO:continuant.
James Malone
bladder carcinoma
DOID:4007
James Malone
oligomycins
CHEBI:25675
GM12044
James Malone
small intestine
MAT:0000047
James Malone
embryonic central brain neuron
FBbt:00005665
James Malone
HCC1428
James Malone
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
James Malone
HCC1569
James Malone
endosperm
MAT:0000227
James Malone
generation
Quality? Is this intrinsic to the organism?
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.
James Malone
juvenile dermatomyositis
DOID:14203
James Malone
glutamine
CHEBI:28300
process
A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
Derived from BFO:processual entity
James Malone
bladder
MAT:0000122
NCI Thesaurus: C12414
James Malone
motoneuron
lateral motoneuron
medial motoneuron
CL:0000100
James Malone
T lymphocyte
T lymphoma cell
CL:0000542
James Malone
GM12043
James Malone
_temp bin organism part
temp holding class to be placed as hierarchy is restructured
James Malone
embryonic central brain mushroom body
FBbt:00005666
James Malone
olmesartan
CHEBI:48416
CS57660
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
James Malone
MCF7
James Malone
brain tumor glioblastoma
James Malone
timepoint
James Malone
polyp
DOID:3475
James Malone
blastula stage
MAT:0000396
James Malone
water
CHEBI:15377
blastula oblong
ZFS:0000013
James Malone
GLI56
James Malone
dopamine
CHEBI:18243
B-cell lymphoma
C3457
James Malone
myocardial infarction
ischaemia
DOID:5844
James Malone
glial cell
mixed glial cells
CL:0000125
James Malone
CS57569
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
James Malone
SUM159PT
James Malone
CS57663
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
James Malone
brain structure
brain
MAT:0000098
NCI Thesaurus: C12439
James Malone
glaucoma
DOID:1686
James Malone
seedhead
MAT:0000237
James Malone
Zinc
CHEBI:27363
polymorphonuclear leukocyte
CL:0000041
James Malone
damage intensity
by a caterpillar on a plant leaf
Measurement of physical damage, e.g. by a caterpillar on a plant leaf
James Malone
cystic fibrosis
DOID:1485
James Malone
blastula high
ZFS:0000012
James Malone
myoblast
nonmesodermal cell
CL:0000056
James Malone
doxorubicin
CHEBI:28748
GLI60
James Malone
B-cell chronic lymphocytic leukemia
DOID:1040
James Malone
CS57570
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
James Malone
SUM185PE
James Malone
time before disease progression
James Malone
breast carcinoma
DOID:3459
James Malone
cervical carcinoma
DOID:2893
James Malone
CS57664
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
James Malone
population
A population is a material entity consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed.
James Malone
damage response
leaf's response to physical damage by a caterpillar on a plant leaf
Physiological response to e.g. leaf's response to physical damage by a caterpillar on a plant leaf
James Malone
cleavage 16-cell
ZFS:0000005
James Malone
GLI72
James Malone
BY4741
James Malone
myeloid cell
CL:0000763
James Malone
dinitrophenol
CHEBI:39352
cytomegalovirus
HCMV
Human Herpesvirus 5
DOID:11259
James Malone
CS57560
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
James Malone
adult eye primordium
FBbt:00005515
James Malone
glioblastoma
DOID:3068
James Malone
SUM190PT
James Malone
CS57816
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
James Malone
time to development of distant metastases
James Malone
MCF12A
James Malone
pool
A mix of specimens from multiple individuals.
James Malone
celiac disease
DOID:10608
James Malone
breast adenocarcinoma
DOID:3458
James Malone
data transformation
A data transformation is a process which produces output data from input data - e.g. the application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
OBI_0200000
James Malone
blastula sphere
ZFS:0000014
James Malone
CS57666
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
James Malone
obsolete_B-lymphocyte
Consolidated with B cell (EFO_0000101), use B cell class instead.
CL:0000236
NCI Thesaurus: C12474
D-mannitol
CHEBI:16899
GM06985
James Malone
CS57563
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
James Malone
SUM225CWN
James Malone
CS57820
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
James Malone
glial cell (sensu Vertebrata)
CL:0000243
James Malone
Arabidopsis thaliana strain
Strain or line specific to Arabidopsis thaliana.
James Malone
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
neoplasia
dedifferentiated chondrosarcoma
DOID:5864
James Malone
portal hypertension
ischaemia
DOID:10762
James Malone
obsolete_test result
Not needed.
The recorded value of the outcome of some test.
CS57646
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
James Malone
genotype
Information, making the distinction between the actual physical material (e.g. a cell) and the information about the genetic content (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.
James Malone
CAMA1
James Malone
Down Syndrome
Down's syndrome
trisomy 21 syndrome
DOID:14250
James Malone
diethylstilbestrol
CHEBI:41922
CS57551
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
James Malone
pharyngula prim-25
ZFS:0000031
James Malone
MCF 10A
James Malone
CS57769
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
James Malone
delivery method
a compound or solution for treatment.
Method used to deliver e.g. a compound or solution for treatment.
time
James Malone
genital system disease
DOID:15
James Malone
porphyria
DOID:13268
James Malone
corpus callosum
NCI Thesaurus: C12446
James Malone
CS57648
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
James Malone
CC531
James Malone
deafness
DOID:10005
NCI Thesaurus: C27644
James Malone
CS57556
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
James Malone
dimethyl sulfoxide
CHEBI:28262
pharyngula prim-15
ZFS:0000030
James Malone
natural killer cell
natural killer
CL:0000623
James Malone
dendritic cell
CL:0000451
James Malone
B-precursor acute lymphoblastic leukemia
James Malone
obsolete_brain tumor glioblastoma
DOID:3074
bone marrow MMHCC
NCI Thesaurus: C22552
James Malone
preeclampsia
ischaemia
DOID:10591
James Malone
CS57655
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
James Malone
somatosensory cortex
NCI Thesaurus: C0037658
James Malone
HMEC184
James Malone
subthalamic nucleus
NCI Thesaurus: C12454
James Malone
diclofenac sodium
CHEBI:4509
pharyngula high-pec
ZFS:0000032
James Malone
experimental autoimmune encephalomyelitis
DOID:3046
James Malone
CFT-2
James Malone
narcolepsy
DOID:8986
James Malone
B-cell acute lymphoblastic leukemia
B-ALL
DOID:7061
James Malone
CS57548
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
James Malone
B-2 B cell
large pre-BII cell
small pre-BII cell
CL:0000822
James Malone
dermal neurofibroma
A dermal neurofibroma is a neurofibroma that occurs in situ of the skin.
James Malone
germ cell tumor
DOID:2994
James Malone
pre-B cell
B-cell precursor
pre-BI cell
CL:0000817
James Malone
obsolete_bone marrow
Duplicate term : see bone marrow EFO_0000868
NCI Thesaurus: C12431
CS57658
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
James Malone
endometriosis
DOID:289
James Malone
SUM149PT
James Malone
synovial membrane
NCI Thesaurus: C12473
James Malone
pharyngula stage
The pharyngula is a developmental stage in embryonic development which follows the blastula, gastrula and neurula stages.
James Malone
myxoid liposarcoma
DOID:5363
James Malone
CSBwt-rescued fibroblasts
James Malone
CS57549
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
James Malone
diethylhexyl phthalate
CHEBI:17747
segmentation 5-9 somites
ZFS:0000024
James Malone
CS57803
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
James Malone
gall tissue
MAT:0000351
James Malone
malaria
DOID:12365
James Malone
occipital lobe
occipital cortex
MAT:0000507
James Malone
acetylsalicylic acid
CHEBI:15365
pons
pons varolii
NCI Thesaurus: C12511
James Malone
CS57896
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
James Malone
familial amyotrophic lateral sclerosis
Familial amyotrophic lateral sclerosis is a amyotrophic lateral sclerosis in which a family history of the disease exists.
James Malone
diffuse scleroderma
DOID:1580
James Malone
digit
MAT:0000285
James Malone
beta cell
beta cell islets
NCI Thesaurus: C32199
James Malone
animal reproductive system
genital system
MAT:0000305
James Malone
CS57807
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
James Malone
segmentation 1-4 somites
ZFS:0000023
James Malone
plant fluid
MAT:0000347
James Malone
control
A control role is borne by a material in a process in which results obtained from an experimental sample and a control sample are compared.
control
reference sample
NCI Thesaurus: C61299
James Malone
parasitic Infection
DOID:1398
NCI Thesaurus: C27864
James Malone
axilla
armpit
underarm
NCI Thesaurus: C12674
James Malone
parietal lobe
MAT:0000506
James Malone
diffuse_large_B-cell_lymphoma
B-cell lymphoma dlbcl
C3457
James Malone
CS57901
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
James Malone
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.
James Malone
neural crest cell
CL:0000333
James Malone
obsolete_biomaterial factor
redundant use material entity
cleavage 8-cell
ZFS:0000004
James Malone
forelimb
upper limb
MAT:0000394
James Malone
leaf
MAT:0000234
James Malone
segmentation stage
James Malone
CS57790
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
James Malone
frontal lobe
MAT:0000505
James Malone
femur
thigh bone
NCI Thesaurus: C12717
James Malone
uninfected
Uninfected class is a disposition in which the bearer is not known to be affected by a disease withtin the context of a study
NCI Thesaurus: C14165
James Malone
obsolete_digit
Duplicated class, use digit EFO_000088.
NCI Thesaurus: C40186
CS57904
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
James Malone
MDAMB231
James Malone
integumental system
MAT:0000033
James Malone
nervous system disease
NCI Thesaurus: C12755
James Malone
SALK_037727
SALK_037727 is an Arabidopsis thaliana strain as described in TAIR http://www.arabidopsis.org/servlets/TairObject?type=germplasm&id=4640315
Germplasm:4640315
James Malone
biopsy number
A biopsy number is an information entity about the numerical label given to a partciular biopsy obtained.
James Malone
pharyngula prim-5
ZFS:0000029
James Malone
CS57801
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
James Malone
shoot
MAT:0000009
James Malone
inguinal region
iliac region
NCI Thesaurus: C12726
James Malone
nutritional disorder
DOID:374
James Malone
CS57905
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
James Malone
CS57644
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
James Malone
digestive system disease
DOID:27
James Malone
telencephalon
MAT:0000421
James Malone
animal body part
MAT:0000293
James Malone
biopsy site
The physical site from which tissue has been removed from a living organism.
James Malone
limb bone
limb skeleton
MAT:0000151
James Malone
infant
juvenile stage
MIAA:0000402
James Malone
nerve cell
neuroblastoma cell
CL:0000540
James Malone
NCI Metathesaurus
tumor
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).
tumour
James Malone
Breast_Tumor_Luminal
humerus
NCI Thesaurus: C12731
James Malone
disease factor
A disease factor is a clinical factor that describes states of disease associated with a particular sample and/or organism.
James Malone
seed
seedling
MAT:0000008
James Malone
CS57812
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
James Malone
Barrett's esophagus
DOID:9206
James Malone
GM06993
James Malone
Epstein-Barr virus infection
EBV infection
DOID:2938
James Malone
metformin
CHEBI:6801
cleavage 32-cell
ZFS:0000006
James Malone
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
James Malone
diencephalon
MAT:0000420
James Malone
CS57908
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
James Malone
MDAMB-157
James Malone
GM12750
James Malone
wing
MAT:0000202
James Malone
dilated cardiomyopathy
DOID:12930
James Malone
pulmonary artery
NCI Thesaurus: C12774
James Malone
ulcerative colitis
DOID:8577
James Malone
meristem
Meristem is a plant component consisting of undifferentiated plant issue - the botanical equivalent of animal stem cells.
MAT:0000006
James Malone
CS57813
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
James Malone
BY4741
James Malone
GM06994
James Malone
idiopathic pulmonary fibrosis
cryptogenic fibrosing alveolitis
NCI Thesaurus: C35716
James Malone
methamphetamine
CHEBI:6809
behaviour
I am trying to determine the difference between a process and a behaviour. Is behaviour dancing any different from the process dancing?
Fixed action pattern courtship behaviour in Drosophila. Forager behaviour in honey bees.
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.
James Malone
cleavage 2-cell
ZFS:0000002
James Malone
thalamus
MAT:0000109
James Malone
CS57923
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
James Malone
MDAMB175VII
James Malone
GM12717
James Malone
haltere
balancer organ
FBbt:00004783
MAT:0000203
James Malone
CS57810
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
James Malone
mesothelial cell
CL:0000077
James Malone
CS57572
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
James Malone
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.
James Malone
idiopathic cardiomyopathy
NCI Thesaurus: C53654
James Malone
segmentation 14-19 somites
ZFS:0000026
James Malone
polycystic ovary syndrome
DOID:11612
James Malone
behavioural stimulus
avoidance
A treatment applied to a sample where some behaviour is expected as a result e.g. avoidance
James Malone
cleavage 64-cell
ZFS:0000007
James Malone
MDAMB134VI
James Malone
hindlimb
lower limb
MAT:0000395
James Malone
post-traumatic stress disorder
posttraumatic stress disorder
traumatic neurosis
DOID:2055
NCI Thesaurus: C3389
James Malone
CS57924
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
James Malone
CS57811
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
James Malone
treatment
disease free survival
Period after successful treatment in which there is no appearance of the symptoms or effects of the disease.
James Malone
hereditary leiomyomatosis and renal cell cancer
HLRCC
NCI Thesaurus: C51302
James Malone
segmentation 10-13 somites
ZFS:0000025
James Malone
benign prostatic hyperplasia
DOID:11131
James Malone
cleavage 4-cell
ZFS:0000003
James Malone
invertebrate limb
invertebrata limb
MAT:0000095
James Malone
type I diabetes mellitus
diabetes mellitus type 1
DOID:9744
James Malone
CS8581
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
James Malone
MDAMB157
James Malone
zeugopod
The middle part of the limb (e.g. between the elbow and wrist)
MAT:0000092
James Malone
chronic lymphocytic leukemia
CLL
DOID:1040
James Malone
motexafin gadolinium
CHEBI:50161
stomach
MAT:0000051
James Malone
GM12239
James Malone
nervous system
MAT:0000026
James Malone
liposarcoma
DOID:3382
James Malone
Aeromonas hydrophila infection
Aeromonas hydrophila infection is a bacterial disease caused by infection from the Aeromonas hydrophila bacteria.
NCI Metathesaurus: C0085491
James Malone
1-naphthyl isothiocyanate
CHEBI:35455
clear cell sarcoma of the kidney
DOID:4880
James Malone
HMEC
James Malone
family based study
NCI Thesaurus:C15407
James Malone
Tomasz Adamusiak
autopod
The generic name for hand, paw, foot, etc.
foot
hand
paw
MAT:0000091
James Malone
obsolete_CTL sensitivity
larynx
MAT:0000187
James Malone
mono-2-ethylhexyl phthalate
CHEBI:17243
GM12248
James Malone
human granulocytic anaplasmosis
Human granulocytic ehrlichiosis
MedlinePlus: 001381
NCI Metathesaurus: C0483368
James Malone
light
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
James Malone
muscle system
muscular system
MAT:0000025
James Malone
obsolete_clinical factor
Redundant
A clincal factors is a biomaterial factor that concerns the observation, treatment or measurement of disease within subjects.
James Malone
HMEC S1
James Malone
vertebrate limb
vertebrata limb
MAT:0000090
James Malone
cross sectional study
NCI Thesaurus:C53310
James Malone
Tomasz Adamusiak
GM12249
James Malone
methyl methanesulfonate
CHEBI:25255
oesophagus
esophagus
MAT:0000048
James Malone
17alpha-estradiol
CHEBI:17160
gametophyte
MAT:0000004
James Malone
tuberculosis
DOID:399
James Malone
liver and biliary system
MAT:0000024
James Malone
clinical history
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
James Malone
embryonic cuprophilic cell
FBbt:00005625
James Malone
disease staging
Dukes C stage describing colon cancer
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
James Malone
GM12716
James Malone
case control study
NCI Thesaurus:C15197
James Malone
Tomasz Adamusiak
fin
MAT:0000087
James Malone
pharynx
MAT:0000049
James Malone
methotrexate
CHEBI:44185
17beta-estradiol
CHEBI:16469
root
MAT:0000005
James Malone
Whipple's disease
DOID:8476
James Malone
obsolete_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.
GM12155
James Malone
Lewis
RGD:737932
James Malone
skeleton
skeletal system
MAT:0000032
James Malone
study design
twin study
A study type is an experimental factor describing the method of investigating particular types of research questions or solving particular types of problems.
PERSON: James Malone
James Malone
N-nitrosodimethylamine
CHEBI:35807
disease state
Acute Lymphocytic Leukemia
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
James Malone
pneumococos infection
DOID:9805
James Malone
embryonic dorsal epidermis
FBbt:00005744
James Malone
(+)-alpha-tocopherol
CHEBI:18145
obsolete_clinical information
epithalamus
MAT:0000422
James Malone
leukemia
DOID:1240
James Malone
seminal vesicle
MAT:0000171
James Malone
Alzheimer's disease
DOID:10652
James Malone
GM12156
James Malone
Sprague Dawley
RGD:70508
James Malone
sensory system
MAT:0000031
James Malone
bipolar disorder
DOID:3312
James Malone
ischemic cardiomyopathy
Ischemic cardiomyopathy is a cardiomyopathy in which a weakness in the muscle of the heart due to inadequate oxygen delivery to the myocardium with coronary artery disease being the most common cause.
WEB:http://en.wikipedia.org/wiki/Cardiomyopathy#Ischemic_cardiomyopathy
James Malone
distant metastasis free survival
James Malone
nifedipine
CHEBI:7565
embryonic dorsal apodeme
FBbt:00005745
James Malone
midbrain
mesencephalon
MAT:0000106
James Malone
clinical treatment
radiotherapy
The current clinical treatment(s) of the patient from which the biosource is derived. E.g. radiotherapy
James Malone
temporal lobe epilepsy
DOID:3328
James Malone
penis
MAT:0000186
James Malone
Leiomyosarcoma
DOID:1967
James Malone
1-(2,4-dichlorobenzyl)-1H-indazole-3-carboxylic acid
CHEBI:50138
respiratory system
MAT:0000030
James Malone
GM12234
James Malone
tooth
MAT:0000041
James Malone
WKY
RGD:61103
James Malone
dorsal apodeme specific anlage
FBbt:00005476
James Malone
N-benzyladenine
CHEBI:29022
masseter muscle
NCI Thesaurus: C13074
James Malone
visual cortex
MAT:0000509
James Malone
aspirin
CHEBI:15365
malignant pleural mesothelioma
DOID:7474
James Malone
Leydig cell
testis - leydig cell
CL:0000178
James Malone
embryonic esophageal ganglion
FBbt:00005670
James Malone
testis
testicle
male gonad
MAT:0000131
James Malone
clypeo-labral primordium
FBbt:00005538
James Malone
GM12236
James Malone
renal system
MAT:0000027
James Malone
Dahl salt-sensitive
RGD:1582190
James Malone
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
James Malone
N-acetyl-L-cysteine
CHEBI:28939
stylopod
The proximal part of the limb (e.g. between shoulder and elbow)
MAT:0000093
James Malone
encephalomyelitis
DOID:640
James Malone
ectoderm
FBbt:00005428
James Malone
temporal lobe
MAT:0000508
James Malone
quercetin
CHEBI:16243
(+)-abscisic acid
CHEBI:2365
embryonic epipharynx
FBbt:00005614
James Malone
leukocyte
white blood cell
leucocyte
CL:0000738
James Malone
ejaculatory duct
MAT:0000170
James Malone
cochlea
MAT:0000144
NCI Thesaurus: C12395
James Malone
cochlear hair cell
CL:0000202
James Malone
adult muscle precursor primordium
FBbt:00005516
James Malone
CS57544
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
James Malone
embryonic foregut
FBbt:00005606
James Malone
knock in expression
Knock in expression is a process in which a gene is replaced by an altered version of the same gene using homologous recombination resulting in a gain of function.
James Malone
developmental stage
puberty
A developmental stage is some identifiable period in an organism's life cycle e.g. puberty
James Malone
obsolete_platform
obsolete platform because the distinction between instrument and platform is very fuzzy
The specific version (such as manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment.
glioma
DOID:2627
James Malone
cirrhosis of liver
DOID:5082
James Malone
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
James Malone
TERV
James Malone
taste system
gustatory system
MAT:0000275
James Malone
age
3 days post planting
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).
James Malone
embryonic esophagus
FBbt:00005612
James Malone
cockayne syndrome
DOID:2962
James Malone
keratinocyte
CL:0000312
James Malone
plexiform neurofibroma
DOID:5151
James Malone
glutamatergic neuron
CL:0000679
James Malone
HCC38
James Malone
liver disease
DOID:409
James Malone
transcription profiling
A transcription profiling is an experiment type in which the transcriptome of a biological sample is analysed.
ArrayExpress production team
James Malone
dermatomyositis
DOID:10223
James Malone
aicardi syndrome
DOID:8461
James Malone
embryonic frontal ganglion
FBbt:00005668
James Malone
large cell neuroendocrine carcinoma
DOID:5721
James Malone
granulocyte
CL:0000094
James Malone
HCC70
James Malone
ploidy
haploid, diploid, triploid
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
James Malone
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
James Malone
sepsis
DOID:2288
James Malone
embryonic foregut sensory structure
FBbt:00005616
James Malone
alveolar rhabdomyosarcoma
DOID:4051
James Malone
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
James Malone
HEK-293H
James Malone
HEK293
James Malone
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.
James Malone
male inflorescence
MAT:0000316
James Malone
HEK293T
James Malone
adult foregut precursor
FBbt:00005611
James Malone
SUM52PE
James Malone
tongue
MAT:0000040
James Malone
female inflorescence
MAT:0000317
James Malone
dexamethasone
CHEBI:41879
HeLa
James Malone
SUM44PE
James Malone
adult hindgut precursor
FBbt:00005646
James Malone
embryonic ganglion mother cell
FBbt:00001433
James Malone
intestine
gut
MAT:0000043
James Malone
neuroblast (sensu Vertebrata)
adrenal neuroblast
CL:0000337
James Malone
CS57671
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
James Malone
desferrioxamine B
CHEBI:4356
phyllid
MAT:0000276
James Malone
Malpighian tubule
FBbt:00005725
MAT:0000123
James Malone
HepaRG
James Malone
cytochalasin B
CHEBI:23527
cranium
gustatory system
MAT:0000340
James Malone
leaf vascular tissue
MAT:0000276
James Malone
adult midgut precursor
FBbt:00000449
James Malone
HepG2
James Malone
retina
MAT:0000142
James Malone
cysteine
CHEBI:17561
T47D
James Malone
stomatal complex
MAT:0000346
James Malone
corpus cardiacum
FBbt:00001717
James Malone
adult
MAT:0000403
James Malone
CS57710
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
James Malone
tomatidine
CHEBI:9629
strain
this class was originally 'strain or line'
A population or type of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
line
James Malone
obsolete_phenotypic factor
phenotype is synonymous with quality
ventricle
cardiac ventricle
MAT:0000497
NCI Thesaurus: C12730
James Malone
CS57596
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
James Malone
sarcoma
Type of cancer of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue.
DOID:1115
James Malone
RAW264.7
James Malone
fludrocortisone
CHEBI:50885
GM11830
James Malone
corpus striatum
dorsal striatum
NCI Thesaurus: C12448
James Malone
mixed sex population
The total number of individuals inhabiting a particular region or area.
James Malone
phenotype
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.
James Malone
strain factor
James Malone
cardiac myocyte
CL:0000746
James Malone
CS57598
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
James Malone
schizophrenia
DOID:5419
James Malone
RKO
James Malone
flufenamic acid
CHEBI:42638
mating type alpha
MO_637
James Malone
GM11831
James Malone
tomatine
CHEBI:9630
pertussis
whooping cough
DOID:1116
James Malone
thioridazine
CHEBI:9566
cardiac mesoderm primordium
FBbt:00005541
James Malone
CS57706
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
James Malone
stroke
ischaemia
DOID:3455
James Malone
CS57601
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
James Malone
hereditary spastic paraplegia
DOID:2476
James Malone
129X1/SvJ
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
129X1
http://jaxmice.jax.org/strain/000691.html
James Malone
formaldehyde
CHEBI:16842
GM07357
James Malone
tolbutamide
CHEBI:27999
CS57709
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
James Malone
cardiac atrium
atrial chamber
NCI Thesaurus: C12728
James Malone
subarachnoid hemorrhage
ischaemia
DOID:11236
James Malone
hepatocyte
CL:0000182
James Malone
sarcoidosis
DOID:11335
James Malone
R8
James Malone
GM11829
James Malone
forskolin
CHEBI:42471
hemopoietic stem cell
hematopoietic stem cell
CL:0000037
James Malone
carcinoma
A type of malignant cancer that arises from epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases.
James Malone
platelet
CL:0000233
James Malone
CS57704
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
James Malone
plasma cell leukemia
James Malone
Crohn's disease
DOID:4039
James Malone
GM07056
James Malone
BALB/c
BALB/c is a mouse strain of albion mice.
http://en.wikipedia.org/wiki/BALB/c
James Malone
ethene
CHEBI:18153
CS57586
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
James Malone
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
PATO:0000047
James Malone
leprosy
DOID:1024
James Malone
DP thymocyte
nontransformed thymocyte
thymocyte
CL:0000809
James Malone
hemopoietic progenitor cell
CL:0000037
James Malone
cancer site
This will be obsoleted in near future.
Location of cancer, primary or metastatic
James Malone
plasmacytoid dendritic cell
CL:0000784
James Malone
hypopituitarism
DOID:9406
NCI:C62591
James Malone
CS57705
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
James Malone
crystal cell
FBbt:00001690
James Malone
129xC57BL/6
129xC57BL/6 is a substrain of the mouse strain 129 as described in article PUBMED ID 15015938
129xC57BL/6
PUBMED ID: 15015938
James Malone
GM07345
James Malone
CS57587
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
James Malone
shear stressing
A process whereby a stress state is applied parallel or tangential to a face of the material.
James Malone
ethyl nitrosourea
CHEBI:23995
Peyer's patch
NCI Thesaurus:C22562
James Malone
stigma
MAT:0000524
James Malone
DEL cells
ZFA:0000711
James Malone
plasma cell
multiple myeloma tumour cell
CL:0000786
James Malone
cancer
ductal carcinoma in situ
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.
James Malone
CS57699
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
James Malone
hematological neoplasm
haematological neoplasm
DOID:253
James Malone
corpus uteri
NCI Thesaurus: C12316
James Malone
toxin
CHEBI:27026
fisetin
CHEBI:42567
C57BL/10
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
James Malone
juvenile days 30-44
ZFS:0000042
James Malone
GM07034
James Malone
plant ovary
MAT:0000517
James Malone
CS57591
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
James Malone
schwannoma
DOID:3192
James Malone
phyllodes tumor
DOID:2608
James Malone
stamen
MAT:0000515
James Malone
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
James Malone
CS57701
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
James Malone
calpainopathy
limb-girdle muscular dystrophy type 2A
DOID:11724
James Malone
cortex
NCI Thesaurus: C12443
James Malone
flavone
CHEBI:42491
BALB/cByJ
BALB is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/001026.html
http://jaxmice.jax.org/strain/001026.html
James Malone
GM07055
James Malone
juvenile stage
MAT:0000402
James Malone
CS57595
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
James Malone
severe acute respiratory syndrome
DOID:2945
James Malone
carpel
MAT:0000516
James Malone
prefrontal cortex
NCI Thesaurus: C0162783
James Malone
mushroom body
MAT:0000336
James Malone
exposure temperature
The temperature that a biosource is exposed to.
James Malone
CS57677
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
James Malone
sensory system disease
A sensory system disease is a disease which has as location the sensory system.
James Malone
dorsal histoblast nest abdominal
FBbt:00001791
James Malone
ductus deferens
MAT:0000129
James Malone
plant sperm
MAT:0000218
James Malone
larval stage
MAT:0000400
James Malone
CS57824
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
James Malone
sjogren syndrome
DOID:12894
James Malone
myocardium
MAT:0000453
James Malone
atrial fibrillation
DOID:11276
James Malone
Wistar
RGD:10044
James Malone
C57BL/6J
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
James Malone
lipoma
DOID:9291
James Malone
CS57691
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
James Malone
scott syndrome
James Malone
Ewing's sarcoma
DOID:3369
James Malone
temporal measurement
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 spatiotemporal region occupied by the development of a cancer tumor.
A temporal entity is an entity that has temporal parts and that happens, unfolds or develops through time. An occurrent is something which exists over time, rather than existing completely at many times
Derived from BFO: Occurrent
James Malone
medulla oblongata
MAT:0000111
James Malone
endometrium
MAT:0000319
James Malone
lepromatous leprosy
DOID:10887
James Malone
tibialis anterior muscle
FMA:22532
James Malone
thallus
MAT:0000248
James Malone
juvenile days 45-89
ZFS:0000043
James Malone
limb-girdle muscular dystrophy
Erb's muscular dystrophy
DOID:11724
James Malone
CS57825
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
James Malone
C2C12
James Malone
Wistar-Furth
RGD:1357955
James Malone
atrioventricular node
MAT:0000498
NCI Thesaurus: C32161
James Malone
C57BL/6
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
James Malone
CS57692
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
James Malone
monoclonal gammopathy
monoclonal gammopathy of uncertain significance
DOID:7442
James Malone
blastula dome
ZFS:0000015
James Malone
dorsal epidermis primordium
FBbt:00005526
James Malone
FUM1
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
James Malone
pollen
MAT:0000216
James Malone
virus
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_10239
James Malone
tuberculoid leprosy
DOID:1025
James Malone
puberty
NCI Thesaurus:C0034011
James Malone
estrogen
CHEBI:50114
pronephros
MAT:0000117
James Malone
sickle cell disease
DOID:10923
James Malone
larval day 5
ZFS:0000037
James Malone
CS57826
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
James Malone
sperm
male gamete
spermatazoon
MAT:0000131
James Malone
blastula 512-cell
ZFS:0000010
James Malone
Copenhagen
RGD:1358153
James Malone
multipotent stem cell
multipotent adult progenitor cell
CL:0000048
James Malone
obsolete_occurrent
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
An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
atmosphere
The atmospheric conditions used to culture or grow an organism.
James Malone
BT483
James Malone
follicular thyroid adenoma
follicular adenoma
DOID:6204
James Malone
dorsal ectoderm primordium
FBbt:00005527
James Malone
Daudi Burkitt's lymphoma
James Malone
promyelocytic leukemia
James Malone
borderline leprosy
DOID:1023
James Malone
postcentral gyrus
FMA:61896
NCI Thesaurus: C33346
James Malone
pars intercerebralis
MAT:0000337
James Malone
CS57827
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
James Malone
ethanol
CHEBI:16236
signet ring cell carcinoma
DOID:3493
James Malone
larval day 4
ZFS:0000036
James Malone
epididymus
MAT:0000130
James Malone
pollen tube
MAT:0000217
James Malone
mouse strain
Strain or line specific to mouse
James Malone
lymphatic system
MAT:0000197
James Malone
atopic eczema
DOID:2771
James Malone
blastula 30%-epiboly
ZFS:0000016
James Malone
BT549
James Malone
Ewing family tumor
DOID:3369
James Malone
dorsal ectoderm anlage in statu nascendi
FBbt:00005832
James Malone
Wistar-Kyoto
RGD:1359002
James Malone
precursor T lymphoblastic leukemia
James Malone
colorectal carcinoma
James Malone
apical root meristem
MAT:0000220
James Malone
larval day 14-20
ZFS:0000040
James Malone
CS57828
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
James Malone
laryngopharynx
hypopharynx
NCI Thesaurus: C12246
James Malone
Syracuse High Avoidance
RGD:1578695
James Malone
time of survival
Time of survival is an information entity which is about the length of time a material entity has survived after some adverse event, such as infection from a disease.
PERSON: James Malone
James Malone
placenta
MAT:0000279
James Malone
T cell
Th1
Th2
pancreatic T effector cell
CL:0000084
James Malone
gastric carcinoma
gastric cancer
DOID:9138
James Malone
tegmentum
MAT:0000452
James Malone
astrocytic tumor
DOID:3069
James Malone
fibromatosis
C3042
James Malone
obsolete_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.
lymph
MAT:0000055
James Malone
blastula 256-cell
ZFS:0000009
James Malone
lacrimal gland
NCI Thesaurus: C12346
James Malone
ArrayExpress production team
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
re-sequencing
James Malone
larval day 6
ZFS:0000038
James Malone
CS57834
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
James Malone
survival probability
The probabilty of continuance of life or existence especially under adverse conditions; Probably need a parent survival metric or similar
James Malone
cervical neck region
FMA:9914
MA:0000309
James Malone
Syracuse Low Avoidance
RGD:1578703
James Malone
lymph node
MAT:0000442
James Malone
tectum
MAT:0000451
James Malone
follicle cell
CL:0000477
James Malone
T-cell lymphoblastic lymphoma
James Malone
astrocytoma
DOID:3069
James Malone
muscle cell
CL:0000187
James Malone
Goto-Kakizaki
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
James Malone
mating type a
MO_659
James Malone
muscular dystrophy
DOID:9884
James Malone
phyllid
MAT:0000276
James Malone
ankle
NCI Thesaurus: C32078
James Malone
uvula
FMA:55022
NCI Thesaurus:C12232
James Malone
syndrome
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
James Malone
CS57835
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
James Malone
stage II endometrioid carcinoma
James Malone
Fischer 344
Fisher344 is a rat strain as described in http://www.ratmap.org/ShowStrainDetails.html?strain=72
F344
http://www.ratmap.org/ShowStrainDetails.html?strain=72
James Malone
hindbrain
rhombencephalon
MAT:0000107
James Malone
Okamoto-Aoki
RGD:1581618
James Malone
lymph vessel
lymphatic vessel
MAT:0000443
James Malone
Caco-2
James Malone
larval day 7-13
ZFS:0000039
James Malone
blastula 1k-cell
ZFS:0000011
James Malone
fetal growth restriction
DOID:13294
James Malone
larval day 21-29
ZFS:0000041
James Malone
rhizome
MAT:0000219
James Malone
melanoma
DOID:1909
James Malone
cataract
DOID:83
James Malone
submandibular gland
NCI Thesaurus: C12233
James Malone
dorsal imaginal precursor
FBbt:00005831
James Malone
CS57836
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
James Malone
systemic scleroderma
systemic sclerosis
DOID:418
James Malone
GABAergic neuron
CL:0000617
James Malone
canrenoate
CHEBI:50159
substantia nigra
MAT:0000504
James Malone
Dahl salt-resistant
RGD:1582184
James Malone
stage I endometrioid carcinoma
James Malone
antenna
MAT:0000086
James Malone
asthma
DOID:2841
James Malone
blastula 128-cell
ZFS:0000008
James Malone
fibroblast
mouse embryonic fibroblast
primary dermal fibroblast
CL:0000057
James Malone
kainic acid
CHEBI:31746
cadmium compounds
CHEBI:22978
feature extraction
The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification
James Malone
dorsal metathoracic disc
FBbt:00001779
James Malone
cervical adenocarcinoma
DOID:3702
NCI Thesaurus: C4029
James Malone
neurohemal organ
neurohaemal organ
FBbt:00001717
MAT:0000212
James Malone
GM12815
James Malone
chronic myeloid leukemia
DOID:8552
James Malone
embryonic stem cell
CL:0000352
James Malone
assay
An assay is a process with the objective to create as an output information about a material entity (bearing evaluant role).
OBI_0000070
James Malone
vagina
MAT:0000128
James Malone
hepatocellular adenoma
NCI Thesaurus: C3758
James Malone
brown fat
brown adipose tissue
MAT:0000198
NCI Thesaurus: C22704
James Malone
family history
Relevant aspects of genetic preconditions or family member's clinical history.
James Malone
jasmonic acid
CHEBI:18292
camptothecin
CHEBI:27656
dorsal pharyngeal muscle primordium
FBbt:00005498
James Malone
GM12872
James Malone
hatching gland
MAT:0000180
James Malone
umbilical cord
MAT:0000280
James Malone
chronic obstructive pulmonary disease
DOID:3083
James Malone
embryonic specific part
An embryonic specific part is an organism part which is specific to embryos.
James Malone
spermathecum
MAT:0000168
James Malone
viral disease
A viral disease is a disease factor that is caused primarily by the infection or otherise hosting of a virus.
James Malone
DNA assay
James Malone
fat body sensu amphibia
MAT:0000456
James Malone
linoleic acids
CHEBI:25048
bucladesine
CHEBI:50095
mouth
oral cavity
MAT:0000038
James Malone
GM12813
James Malone
familial combined hyperlipidemia
DOID:13809
James Malone
artery
arterial system
MAT:0000034
James Malone
biceps femoris
NCI Thesaurus: C53147
James Malone
obsolete_thymus
MAT:0000080
embryonic gastric caecum
FBbt:00005629
James Malone
HIV
HIV infection
human immunodeficiency virus
DOID:526
NCI Thesaurus: C3108
James Malone
RNA assay
James Malone
vulva
MAT:0000169
James Malone
lapatinib
CHEBI:38636
ear
auditory system
MAT:0000138
James Malone
butyrate
CHEBI:17968
cervix
MAT:0000292
James Malone
dorsal mesothoracic disc
FBbt:00001778
James Malone
facioscapulohumeral muscular dystrophy
DOID:11727
James Malone
GM12814
James Malone
sciatic nerve
FMA:19034
NCI Thesaurus: C52810
James Malone
pineal gland
MAT:0000448
James Malone
white fat
MAT:0000199
James Malone
protein assay
James Malone
AIDS
acquired immune deficiency syndrome
acquired immunedeficiency syndrome
DOID:635
James Malone
bone marrow
MAT:0000084
James Malone
deltoid
NCI Thesaurus: C32446
James Malone
lipoxin A4
CHEBI:6498
obsolete_dorsal root ganglion
Duplicate use EFO_0000900
NCI Thesaurus: C12462
vein
venous system
MAT:0000037
James Malone
bisphenol A
CHEBI:33216
extraction protocol
DNA/RNA extraction
The procedure used to obtain something from a mixture or compound by chemical or physical or mechanical means, e.g. DNA/RNA extraction
James Malone
GM12763
James Malone
bark
MAT:0000360
James Malone
eye
visual system
MAT:0000140
James Malone
adrenal gland pheochromocytoma
NCI Thesaurus: C3326
James Malone
endometrioid carcinoma
DOID:3000
James Malone
unfertilized egg
female gamete
oocyte
unfertilised egg
MAT:0000124
James Malone
media
probably a role
liquid, agar, soil
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil).
James Malone
circular visceral mesoderm primordium
FBbt:00000107
James Malone
microspore
MAT:0000215
James Malone
mesonephros
MAT:0000118
James Malone
instrument design
James Malone
leg
NCI Thesaurus: C32974
James Malone
meninges
MAT:0000113
James Malone
dorsal trunk specific anlage
FBbt:00005489
James Malone
azoospermia
DOID:14227
James Malone
GM12812
James Malone
heart
MAT:0000036
James Malone
bleomycin A2
CHEBI:3139
xylem
MAT:0000363
James Malone
lipopolysaccharide
CHEBI:16412
James Malone
nose
olfactory system
MAT:0000139
endocarditis
DOID:10314
James Malone
mature B cell
721 B lymphoblasts
CL:0000785
James Malone
animal ovary
MAT:0000125
James Malone
circular visceral muscle fibers
FBbt:00005072
James Malone
kidney
metanephros
MAT:0000119
James Malone
megaspore
MAT:0000214
James Malone
analyte
Analyte role is a role borne by a material entity and realized by implementation of an analyte measuring assay with objective to detect the magnitude/concentration/ amount of the analyte in the entity bearing evaluant role.
OBI_0000275
James Malone
autoimmune pancreatitis
DOID:4989
James Malone
lithium chloride
CHEBI:48607
dorsal prothoracic pharyngeal muscle
FBbt:00000489
James Malone
embryonic gonadal ridge
NCI Thesaurus: C34184
James Malone
GM12761
James Malone
carotid artery
MAT:0000501
James Malone
azathioprine
CHEBI:2948
TBP-105Q
TBP-105Q is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/008075.html
JAX:8075Â Â Â Â
James Malone
asbtestos
CHEBI:46661
adrenal cortex
MAT:0000494
NCI Thesaurus: C12396
James Malone
oviduct
fallopian tube
uterine tube
MAT:0000126
James Malone
CS57823
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
James Malone
obsolete_material type
redundant now and is synonymous to material type.
population of an organism, organism, organism part, cell
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
malignant peripheral nerve sheath tumor
DOID:5940
James Malone
emphysema
NCI Thesaurus: C3348
James Malone
DNA
DNA is a chemical compound which has a high molecular weight, linear polymers and is composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contains the genetic information of organisms.
deoxyribonucleic acid
CHEBI:16991
James Malone
chronic pancreatitis
DOID:13315
James Malone
plant egg
MAT:0000213
James Malone
gastrocnemius
NCI Thesaurus:C32666
James Malone
lisinopril
CHEBI:43755
dorsal ridge
FBbt:00000090
James Malone
B6C3F1
B6C3F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100010.html
JAX:100010
James Malone
GM12762
James Malone
stem
MAT:0000239
James Malone
atrium
FBbt:00005615
MAT:0000496
James Malone
blood vessel
MAT:0000393
James Malone
bis(2-chloroethyl) sulfide
CHEBI:25434
CS57822
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
James Malone
male germ cell
testis - germ cell
CL:0000015
James Malone
adrenal gland
MAT:0000071
NCI Thesaurus: C12666
James Malone
uterus
uterine horn
MAT:0000127
James Malone
spleen
MAT:0000085
James Malone
RNA
RNA is a chemical compound which are naturally occurring polyribonucleotides.
ribonucleic acid
CHEBI:33697
James Malone
normal
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.
James Malone
reference sample
control
Emery-Dreifuss muscular dystrophy
DOID:11726
James Malone
cingulate cortex
cingulate cortex homogenate
NCI Thesaurus: C52713
James Malone
GM07022
James Malone
IB3-1
James Malone
clear cell adenocarcinoma
DOID:4468
James Malone
macrophage
bone marrow-derived macrophage
monocyte-derived macrophage
CL:0000235
James Malone
CS57580
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
James Malone
adipose tissue MMHCC
NCI Thesaurus: C22703
James Malone
troglitazone
CHEBI:9753
apoplasm
MAT:0000348
James Malone
GM12751
James Malone
hydrostatic pressure
The pressure exerted by a liquid as a result of its potential energy, ignoring its kinetic energy.
James Malone
HT-29
James Malone
experiment performer
An individual who does some experimental process.
James Malone
mesalamine
CHEBI:6775
cutaneous melanoma
cancer of skin
skin melanoma
DOID:8923
James Malone
obsolete_processual entity
GM07000
James Malone
IMR-32
James Malone
lymphoma
DOID:353
James Malone
SUM1315MO2
James Malone
clear cell renal carcinoma
DOID:4467
James Malone
obsolete_adipose tissue brown MMHCC
Made obsolete: use brown fat EFO_0000812 instead
brown fat
bulbus arteriosus
NCI Thesaurus: C22704
environmental factor
This should become a material entity with the role of environment
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
environment factor
James Malone
trifluoperazine
CHEBI:45951
nectar
MAT:0000349
James Malone
GM12760
James Malone
mercaptopurines
CHEBI:35666
hyperglycemia
hyperglycaemia
DOID:4195
James Malone
electrical current
Formerly class "current milliamperes"
The measure of movement of electrical charges in a conductor measured in milliamperes.
James Malone
period of infection
James Malone
lymphocyte
CL:0000542
James Malone
adenosquamous lung carcinoma
DOID:4829
James Malone
classical Hodgkin's lymphoma
C7164
James Malone
CS57583
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
James Malone
obsolete_environment
Synonym of environmental factor
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
James Malone
arm
NCI Thesaurus: C32141
James Malone
wood parenchyma
MAT:0000365
James Malone
cultivar
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.
James Malone
obsolete_percent oxygen
trichostatin A
CHEBI:46024
HMT3522S1
James Malone
host
An animal or plant or part thereof that nourishes and supports a parasite either in a lab or natural environment.
James Malone
lymphoblast
NCI Thesaurus: C13013
James Malone
SKGT4
James Malone
classifier prediction
An extrapolation into the future of data into a class with specified label.
James Malone
adipose tissue
NCI Thesaurus: C12472
James Malone
endothelial cell
lymphatic endothelial cell
primary lymphatic endothelial cell
CL:0000115
James Malone
CS57581
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
James Malone
crystal cell specific anlage
FBbt:00005463
James Malone
phloem
MAT:0000364
James Malone
obsolete_percent oxygen concentration
HS578T
James Malone
Huntington's disease
DOID:12858
James Malone
SKBR3
James Malone
protein
RNA is a chemical compound which are naturally occurring polyribonucleotides.
ribonucleic acid
PRO:000000001
James Malone
L3055
James Malone
adenoid cystic carcinoma
DOID:4866
James Malone
bronchoalveolar adenocarcinoma
DOID:4926
James Malone
lung adenocarcinoma
DOID:3910
James Malone
corm
MAT:0000368
James Malone
estradiol
CHEBI:16469
Vitamin D3
CHEBI:27300
hippocampus
MAT:0000114
NCI Thesaurus: C22615
James Malone
doxycycline
CHEBI:50845
pericardium
MAT:0000454
James Malone
lobular breast carcinoma
DOID:3457
James Malone
adenoma
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
James Malone
LY2
James Malone
Burkitt's lymphoma
DOID:8584
James Malone
morphology
Microscopic morphology of tissues.
histology
James Malone
Vanadium
CHEBI:27698
fat body sensu invertebrata
MAT:0000096
James Malone
endocardium
MAT:0000455
James Malone
IMR-90
James Malone
S49
SchneiderSL2
James Malone
periodontitis
DOID:824
James Malone
breast tumor luminal
James Malone
sap
MAT:0000350
James Malone
valproic acid
CHEBI:39867
Kin-S49
James Malone
S2
James Malone
adenohypophysis
ZFA:0001282
James Malone
bulb
MAT:0000367
James Malone
bronchial epithelium
C32231
James Malone
uniconazole-P
CHEBI:38000
is_input_of
ro:contains
has_input
realizes
Relation between a process and a material fulfilling a role (i.e. realizing a role within the context of the process). For example a human realizing role of teacher within a lesson teching process.
is_realized_by
is_role_of
relationship
has_quality
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t.
ro:contained_in
has_role
has_part
EFO_0000823
part_of
EFO_0000822
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.)
derives_from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it 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. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
derived_into
inheres_in
bearer_of
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
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
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
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
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
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
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 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
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
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 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
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
A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
GOC:cjm
http://purl.org/obo/owl/GOC#GOC_cjm
derived_from