Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.

  0: asymptomatic
  100: asymptomatic
  1: symptomatic but fully ambulatory
  2: symptomatic but in bed less than 50% of the day
  3: symptomatic in bed more than 50% of the day but not bed ridden
  40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
  4: bed ridden
  60-70: symptomatic but in bed less than 50% of the day
  80-90: symptomatic but fully ambulatory
  ACS
  AES Chemunex
  Advanced Instruments Inc. (AI Companies)
  Affymetrix
  Affymetrix
  Agilent
  Ambion
  Antigenix
  Apogee Flow Systems
  Applied Biosystems
  Applied Biosystems
  BIO-RAD
  Beckman Coulter
  Becton Dickinson (BD Biosciences)
  Becton Dickinson (BD Biosciences)
  Bentley Instruments
  BioGents
  BioGents
  Bruker Corporation
  Bruker Daltonics
  Compensation-ML
  CytoBuoy
  CytoBuoy
  Cytopeia
  Dako Cytomation
  Edingburgh handedness inventory
  Edingburgh handedness inventory
  Exalpha Biological
  Exbio Antibodies
  FCS
  G1 (Fuhrman)
  G1 (WHO)
  G1: Well differentiated
  G2 (Fuhrman)
  G2 (WHO)
  G2: Moderately differentiated
  G3 (Fuhrman)
  G3 (WHO)
  G3: Poorly differentiated
  G4 (Fuhrman)
  G4 (WHO)
  G4: Undifferentiated
  Gating-ML
  GenePattern CART
  GenePattern HeatMapViewer data visualization
  GenePattern HierarchicalClusteringViewer data visualization
  GenePattern LOOCV
  GenePattern PCA
  GenePattern SVM
  GenePattern hierarchical clustering
  GenePattern k-means clustering
  GenePattern k-nearest neighbors
  GenePattern module CARTXValidation
  GenePattern module HeatMapViewer
  GenePattern module HierarchicalClustering
  GenePattern module HierarchicalClusteringViewer
  GenePattern module KMeansClustering
  GenePattern module KNN
  GenePattern module KNNXValidation
  GenePattern module PCA
  GenePattern module PeakMatch
  GenePattern module SVM
  GenePattern peak matching
  Helicos
  Helicos
  High grade ovarian tumor
  Illumina
  Illumina
  Invitrogen
  Li-Cor
  Li-Cor
  Low grade ovarian tumor
  Luminex
  Millipore
  Miltenyi Biotec
  NanoString Technologies
  NanoString Technologies
  Nimblegen
  Nimblegen
  OWL
  Occult Carcinoma (AJCC 7th)
  Oxford Nanopore Technologies
  Oxford Nanopore Technologies
  Pacific Biosciences
  Pacific Biosciences
  Partec
  RDF
  Roche
  Roche
  Stage 0 (AJCC 7th)
  Stage 1 (FIGO)
  Stage 1A (FIGO)
  Stage 1B (FIGO)
  Stage 1C (FIGO)
  Stage 2 (FIGO)
  Stage 2A (FIGO)
  Stage 2B (FIGO)
  Stage 2C (FIGO)
  Stage 3 (FIGO)
  Stage 3A (FIGO)
  Stage 3B (FIGO)
  Stage 3C (FIGO)
  Stage 4 (FIGO)
  Stage I (AJCC 7th)
  Stage IA (FIGO)
  Stage IA1 (FIGO)
  Stage IA2 (FIGO)
  Stage IB (FIGO)
  Stage IB1 (FIGO)
  Stage IB2 (FIGO)
  Stage IIA (AJCC 7th)
  Stage IIA (FIGO)
  Stage IIA1 (FIGO)
  Stage IIA2 (FIGO)
  Stage IIB (AJCC 7th)
  Stage IIB (FIGO)
  Stage IIC (AJCC 7th)
  Stage IIIA (AJCC 7th)
  Stage IIIA (FIGO)
  Stage IIIB (AJCC 7th)
  Stage IIIB (FIGO)
  Stage IIIC (AJCC 7th)
  Stage IVA (AJCC 7th)
  Stage IVA (FIGO)
  Stage IVB (AJCC 7th)
  Stage IVB (FIGO)
  Stage Unknown (FIGO)
  Sysmex Corporation, Kobe, Japan
  Sysmex Corporation, Kobe, Japan
  Thermo
  Thermo Fisher Scientific
  Transformation-ML
  U.S. Food and Drug Administration
  Waters
  XML
  ambidexterous
  angstrom
  axiom holds for all times
  cM0 (colon)
  cM0 (kidney)
  cM0 (lung)
  cM0 (ovary)
  cM1 (colon)
  cM1 (kidney)
  cM1 (lung)
  cM1 (ovary)
  cM1a (colon)
  cM1a (lung)
  cM1b (colon)
  cM1b (lung)
  centimeter
  colony forming unit per volume
  count per molar
  count per molar second
  count per nanomolar
  count per nanomolar second
  cubic centimeter
  cubic decimeter
  day
  defined class
  degree Celsius
  degree Fahrenheit
  eBioscience
  example to be eventually removed
  failed exploratory term
  geographic location
  gram
  gram per deciliter
  gram per liter
  hertz
  hour
  iao.owl
  kilogram
  left handed
  liter
  mass percentage
  mass volume percentage
  metadata complete
  metadata incomplete
  meter
  microgram
  microgram per liter
  microliter
  microliters per minute
  micrometer
  micromolar
  micromole
  milligram
  milligram per milliliter
  milliliter
  milliliter per liter
  millimeter
  millimolar
  minute
  molar
  month
  named class expression
  nanogram
  nanoliter
  nanometer
  nanomolar
  nanomole
  obi.owl
  obsolete_core
  obsolete_manufacturer role of Bruker Corporation
  obsolete_manufacturer role of Bruker Daltonics
  obsolete_manufacturer role of applied biosystems
  obsolete_other
  obsolete_the manufacturer role of Agilent
  obsolete_the manufacturer role of Ambion
  obsolete_the manufacturer role of BIO-RAD
  obsolete_the manufacturer role of Helicos
  obsolete_the manufacturer role of Illumina
  obsolete_the manufacturer role of Li-Cor
  obsolete_the manufacturer role of Roche
  obsolete_the manufacturer role of Thermo
  obsolete_the manufacturer role of Waters
  obsolete_the regulator role of the FDA
  obsolete_the supplier role of Affymetrix
  organizational term
  pH
  pM1 (colon)
  pM1 (kidney)
  pM1 (lung)
  pM1 (ovary)
  pM1a (colon)
  pM1a (lung)
  pM1b (colon)
  pM1b (lung)
  pN0 (colon)
  pN0 (kidney)
  pN0 (lung)
  pN0 (ovary)
  pN1 (colon)
  pN1 (kidney)
  pN1 (lung)
  pN1 (ovary)
  pN1a (colon)
  pN1b (colon)
  pN1c (colon)
  pN2 (colon)
  pN2 (lung)
  pN2a (colon)
  pN2b (colon)
  pN3 (lung)
  pT0 (colon)
  pT0 (kidney)
  pT0 (lung)
  pT0 (ovary)
  pT1 (colon)
  pT1 (kidney)
  pT1 (lung)
  pT1 (ovary)
  pT1a (kidney)
  pT1a (lung)
  pT1a (ovary)
  pT1b (kidney)
  pT1b (lung)
  pT1b (ovary)
  pT1c (ovary)
  pT2 (colon)
  pT2 (kidney)
  pT2 (lung)
  pT2 (ovary)
  pT2a (kidney)
  pT2a (lung)
  pT2a (ovary)
  pT2b (kidney)
  pT2b (lung)
  pT2b (ovary)
  pT2c (ovary)
  pT3 (colon)
  pT3 (kidney)
  pT3 (lung)
  pT3 (ovary)
  pT3a (kidney)
  pT3a (ovary)
  pT3b (kidney)
  pT3b (ovary)
  pT3c (kidney)
  pT3c (ovary)
  pT4 (kidney)
  pT4 (lung)
  pT4a (colon)
  pT4b (colon)
  pTis (colon)
  pTis (lung)
  pending final vetting
  picogram
  picoliter
  picomolar
  picomole
  placeholder removed
  ready for release
  relation has no temporal argument
  requires discussion
  right handed
  second
  tar
  term imported
  term split
  terms merged
  to be replaced with external ontology term
  uncurated
  universal
  volume percentage
  week
  year
  zip

Ontology information

Ontology ID: obi
Version: 2022-01-03
Number of terms: 4628
Last loaded: Tue Jan 11 07:16:44 GMT 2022

license

http://creativecommons.org/licenses/by/4.0/

Format

OWL-DL

OBO foundry unique label

Ontology for Biomedical Investigations

Contributor

Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester

comment

Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.

Creator

Eric Deutsch

Richard Scheuermann

Barry Smith

James Malone

Richard Bruskiewich

John Westbrook

Chris Taylor

Dirk Derom

Norman Morrison

Trish Whetzel

Bill Bug

Christian Bolling

Chris Mungall

Kevin Clancy

Elisabetta Manduchi

Ryan R. Brinkman

Bjoern Peters

Philippe Rocca-Serra

Jie Zheng

Melissa Haendel

Larisa Soldatova

Alan Ruttenberg

Holger Stenzhorn

Jennifer Fostel

Frank Gibson

Susanna-Assunta Sansone

Gilberto Fragoso

Allyson Lister

Liju Fan

Tina Hernandez-Boussard

Joe White

Matthew Brush

Melanie Courtot

James A. Overton

Dawn Field

Carlo Torniai

Phillip Lord

Cristian Cocos

Daniel Schober

Daniel Rubin

Helen Parkinson

Pierre Grenon

Monnie McGee

Robert Stevens

Yongqun He

Chris Stoeckert

Mervi Heiskanen

Jeffrey Grethe

Lawrence Hunter

Helen C. Causton

Jessica Turner

Luisa Montecchi

Jay Greenbaum

Stefan Wiemann

Matthew Pocock

Tanya Gray

title

Ontology for Biomedical Investigations

Date

2009-07-31

Subject and Keywords

An ontology for the annotation of biomedical and functional genomics experiments.