== ImmPort ==
This page was initially created to support the ontology work of the Immunology Database and Analysis Portal ([https://immport.niaid.nih.gov/ ImmPort]) portal within the framework of the Bioinformatics Integration Support Contract ([https://www.fbo.gov/index?s=opportunity&mode=form&id=67aa839f87c97f95f7531ba9d86f67b5&tab=core&_cview=1 BISC]), funded by the NIH’s National Institute of Allergy and Infectious Diseases (NIAID). ImmPort is designed to enable scientists to easily access and exchange interoperable complex data sets to accelerate scientific discovery. It provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID. A summary of work so far is provided here:
'''[https://www.nature.com/articles/sdata201815 ImmPort, toward repurposing of open access immunological assay data for translational and clinical research''']
[[File:sdata201815-f1.jpg]]
See also '''[http://ncorwiki.buffalo.edu/index.php/ImmPort_Ontology_Conference ImmPort Ontology Conference]'''
== Background ==
The huge plasticity of the immune response, the strong dependence upon the context in which it occurs and on physiological and pathological conditions, and the wide range of responses elicited, make immunology an especially challenging domain for data integration.
The ontologies documented below are designed to enhance the degree to which immunology research results can be expressed in a consistent fashion across communities and disciplines, thus advancing not only the analysis and integration of data but also its discoverability by scientists who were not involved in its creation. In this way, they will contribute to the realization of the goals of ImmPort to accelerate a more collaborative and coordinated research environment and create an integrated database. that broadens the usefulness of scientific data and advances hypothesis-driven and hypothesis-generating research, as well as the development of optimal methods for data collection, storage, exchange and interoperability.
The team of University at Buffalo ontologists with primary responsibility for this work includes:
*[http://ontology.buffalo.edu/smith Barry Smith], Professor of Philosophy, Neurology and Computer Science and Director of the National Center for Ontological Research.
*[http://medicine.buffalo.edu/faculty/profile.html?ubit=addiehl Alexander Diehl], UB Department of Neurology
*[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg], UB Department of Oral Biology.
For further background see: http://www.buffalo.edu/news/releases/2009/01/9857.html
== Ontologies ==
'''Recommended'''
Chemical Entities of Biological Interest ([http://www.ebi.ac.uk/chebi/ CHEBI]) ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238832/ Paper])
The Protein Ontology ([http://pir.georgetown.edu/pro/ PRO]) [[Immunology Content in the Protein Ontology]] ([https://www.ncbi.nlm.nih.gov/pubmed/24270789 Paper])
The Gene Ontology ([http://www.geneontology.org/ GO])
:[https://academic.oup.com/bioinformatics/article-abstract/23/7/913/217736/Ontology-development-for-biological-systems?redirectedFrom=fulltext Gene Ontology Immunology Branch]
The Cell Ontology ([http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell CL])
:[[Paper on FlowCL]]
The Immune Epitope Ontology ([http://70.167.3.46/iedb/ ONTIE]) ([https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/database/2017/1/10.1093_database_bax014/1/bax014.pdf?Expires=1495567763&Signature=aq0gI9Uu-DUa~usLrASKWTnsl1cZQth0pef5ziCfCcDAxk~lT88lKDwQh90D-xRw8TKRoHWcY3MSzqmq~GJ~Hs9AE6sNjNFSI9l7fftxV6xJ2SAonXWeyv9ITQAYOt-Gdk7anXXDImIX-lbpHF~VHSbjfJ-OAO6iHz6dDyuGLm4lEhcl~gnQSMmw1U~sRo2HiD3AQsEsMSXXsQUgyIYyvQtauYkTWmkSlcFEEnusyNvpwjnsqoVnJ95ceazJj44UJIBKkiMXxiwgq1x71sO~XcPGmYPWJeRFlqlXNftOx5Fw6Nf1MHYim~1CwOPCSCvRmnOmWKNx2d6a5NaLKgA~Sg__&Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q paper])
Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO])
[http://ceur-ws.org/Vol-1747/IP18_ICBO2016.pdf ImmPort Antibody Ontology]
[http://www.violinet.org/vaccineontology/ Vaccine Ontology]
[https://bioportal.bioontology.org/ontologies/OVAE Ontology of Vaccine Adverse Events] ([https://www.ncbi.nlm.nih.gov/pubmed/?term=Ontology+of+Vaccine+Adverse+Events+au%3Ahe Paper])
Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI]) ([https://www.ncbi.nlm.nih.gov/pubmed/27128319 Paper])
Ontology for General Medical Science ([http://code.google.com/p/ogms/ OGMS])
[https://vdjserver.org VDJ Server] [http://www.irmacs.sfu.ca/event/15401 Video]
'''Under development'''
[[Allergy Ontology]]
[http://ontology.buffalo.edu/12/immunology_ontology/Masci%20AM.pdf Immunology Ontology]
== Ontology Consortia ==
[http://www.obofoundry.org/ OBO (Open Biological and Biomedical Ontologies) Foundry]
== Clinical Trial Ontology / CDISC ==
Ravi Shankar, [http://ncor.buffalo.edu/2014/03132014_CTO.pdf Clinical Trial Ontology], March 13, 2014
CDISC Phuse [http://www.phusewiki.org/docs/2010/2010%20PAPERS/CD03%20Paper.pdf paper on LabTests], 2010
[http://www.bioontology.org/wiki/index.php/Workshop_on_Clinical_Trial_Ontology Clinical Trial Ontology Meeting], 2007
[http://cdiscguru.blogspot.com/ CDISC Guru]
== Portals ==
[https://immport.niaid.nih.gov/immportWeb/home/home.do?loginType=full Immunology Database and Analysis (ImmPort) Portal]
[http://bioportal.bioontology.org/ NCBO Bioportal] (ontology repository)
[http://www.ontobee.org/index.php Ontobee] (ontology visualization portal)
[http://www.immuneprofiling.org/hipc/page/showPage?pg=subcommittees-bioinf HIPC: Human Immunology Project Consortium]
[http://tsb.mssm.edu/primeportal/ Program for Research on Immune Modeling and Experimentation PRIME]
[http://www.iedb.org/ Immune Epitope Database and Analysis Resource]
[http://www.imgt.org International ImMunoGeneTics Information System]
== ImmPort Antibody Registry ==
Alex Diehl, [http://ncor.buffalo.edu/2014/Diehl-9-4-14.pdf The ImmPort Antibody Registry and Ontology]
== Cytokines ==
Barry Smith, [http://ncor.buffalo.edu/2014/Smith-Cytokines.pptx The OBO Foundry approach to ontologies and standards with special reference to cytokines]
==Laboratory Information Systems==
Open Source
:[https://labkey.com/ LabKey]
:[https://community.openclinica.com/ OpenClinica]
:[https://wiki.nci.nih.gov/display/caBIGCommunityCode/caLIMS caLIMS] (from NCI)
:[http://www.labmatica.com/ Labmatica]
:[http://bika.sourceforge.net/ Bika]
Proprietary
:[https://www.labware.com/lwweb.nsf/rHome3.xsp LabWare]
:[http://www.mdsol.com/ Medidata]
:[http://www.perkinelmer.com/products/software-informatics/default.xhtml Perkin Elmer]
:[http://ruro.com/ Ruro]
:[http://www.starlims.com/en-us/home/ StarLIMS]
:[http://www.waters.com/waters/en_US/LabWare-LIMS/nav.htm?cid=1000194&locale=en_US LabWare LIMS (Waters)]
Sample process focused:
:[http://www.biofortis.com/ BioFortis]
:[http://www.sampleminded.com/ Sampleminded]
[http://www.starlims.com/de-de/dokumentenbibliothek/white-paper/lis-vs-lims-2/ LIS vs. LIMS]
== Publications ==
Maecker, H., McCoy, J.P. & Nussenblatt, R. [http://www.ncbi.nlm.nih.gov/pubmed/22343568 Standardizing immunophenotyping for the human immunology project]. Nature reviews Immunology 12, 191-200 (2012).
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. , [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration], Nature Biotechnology, 25 (11), November 2007, 1251-1255.
Cowell LG, Smith B, [http://ontology.buffalo.edu/medo/IDO-Chapter.pdf Infectious Disease Ontology], in Vitali Sintchenko, Infectious Disease Informatics, New York: Springer, December 2009, 373-395.
Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG, [http://www.biomedcentral.com/1471-2105/10/70 An improved ontological representation of dendritic cells as a paradigm for all cell types], BMC Bioinformatics, February 2009, 10:70.
Diehl AD, Augustine AD, Blake JA, Cowell LG, et al. [http://www.ncbi.nlm.nih.gov/pubmed/20123131 Hematopoietic cell types: prototype for a revised cell ontology]. J Biomed Inform. 2011; 44(1).
Meehan TF, Masci AM, Abdulla A, Cowell LG, et al. [http://www.ncbi.nlm.nih.gov/pubmed/21208450 Logical development of the cell ontology]. BMC Bioinformatics. 2011; 12.
Goldfain A, Smith B, Cowell LG, [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC293020/ Towards an Ontological Representation of Resistance: The Case of MRSA], Journal of Biomedical Informatics, 2011 (Feb.), 44:1, 35-41.
Scheuermann RH, Ceusters W, Smith B, [http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Toward an Ontological Treatment of Disease and Diagnosis], Proceedings of the 2009 AMIA Summit on Translational Bioinformatics, 2009, 116-120.
Goldfain A, Smith B, Cowell LG, [http://ontology.buffalo.edu/ido/Dispositions_and_IDO.pdf Dispositions and the Infectious Disease Ontology], in Antony Galton and Riichiro Mizoguchi (eds.), Formal Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2010), Amsterdam: IOS Press, 2010, 400-413.
Goldfain A, Smith B, Cowell LG, [http://ontology.buffalo.edu/smith/articles/ICBO2012/IDO_Lattice.pdf Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository]”, Proceeedings of the Third International Conference on Biomedical Ontology, Graz, July 23-25, 2012 (CEUR, vol. 897).
Cox AP, Jensen M, Duncan W, Weinstock-Guttman B, Szigeti K, Ruttenberg A, Smith B, Diehl AD, [http://kr-med.org/icbofois2012/proceedings/ICBOFOIS2012Workshops/ICBO2012MFO/SingleFiles/icbo-2012_MFO_Cox.pdf Ontologies for the Study of Neurological Disease], Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology, Graz, July 22, 2012.
Yu AC, Smith B, Schwartz S, [http://ontology.buffalo.edu/medo/ACAAI-2012.pdf Formal and Computable Representations of Allergic Diseases in the Electronic Health Record: An Approach Based on the Ontology of General Medical Science, 2012 Annual Meeting of the American College of Allergy, Asthma & Immunology (ACAAI), November 8-13, 2012, Anaheim, California (Poster).
== Events ==
June 11-13, 2012
:'''[http://www.bioontology.org/wiki/index.php/Immunology_Ontologies_and_Their_Applications_in_Processing_Clinical_Data Immunology Ontologies and Their Applications in Processing Clinical Data]'''
April 8, 2013
:'''1st ImmPort Ontology Group Web Conference''':
:4:00pm Lindsay Cowell (UT Southwestern): The VDJ Server
:5:00pm General discussion of CL and CyTOF
April 22, 2013
:'''2nd ImmPort Ontology Group Web Conference'''
:4:00pm Nikolay Samusik (Stanford): Charting the reference map of the immune system using CyTOF data
April 29, 2013
:'''3rd Immport Ontology Group Web Conference'''
:4:00pm Yannick Pouliot (Stanford): Peak Probability Contrasts ([http://www-stat.stanford.edu/~tibs/PPC/ PPC])
June 11, 2013
:'''[http://ncorwiki.buffalo.edu/index.php/Immunology_Ontology Lecture and practical session on Immunology Ontology]
:[http://www.bu.edu/computationalimmunology/summerschool/index.html Summer School for Quantitative Systems Immunology], Boston, MA.
June 24, 2013
:'''[[4th Immport Ontology Group Web Conference]]'''
August 1, 2013
:'''[http://ontology.buffalo.edu/smith/ppt/Immunology/ImmPort-Aug-1-2013.pptx How to make ImmPort data fit for secondary use]''', Barry Smith
:Immport Science Group
September 4-5, 2013
:'''[http://ncorwiki.buffalo.edu/index.php/ImmPort_Ontology_Conference ImmPort Ontology Conference]''', Stanford University.
October 3, 2013
[http://ncor.buffalo.edu/2014/Diehl-Ontology-Update-10-3-13.pptx Ontology Update: Antibodies, Proteins Cells], Alexender Diehl
:ImmPort Science Group
Oct 9-10, 2013
:'''[http://ncorwiki.buffalo.edu/index.php/ImmPort Training and Strategy Workshop for ImmPort Data Submitters]''', Rho Federal Systems Division, Chapel Hill, NC, October 9-10
January 21, 2014
:'''[http://www.youtube.com/watch?v=booqxkpvJMg Clinical Trial Data Wants to be Free]
:Presentation by Barry Smith, University at Buffalo Clinical and Research Ethics Seminar
February 27, 2014
:'''[http://ontology.buffalo.edu/smith/ppt/Immunology/BISC-Science-Meeting-Feb-27-2014.pptx Enhancing the Quality of ImmPort Data], Immport Science Group
March 13, 2014
:'''5th ImmPort Ontology Group Web Conference'''
:Presentation by Ravi Shankar on the [http://ncor.buffalo.edu/2014/03132014_CTO.pdf Clinical Trial Ontology]
March 18, 2014
:'''[[Discussion with Labkey]]'''
March 20, 2014
:'''[http://ncor.buffalo.edu/2014/Gene-Expression-and-Identity.pptx Gene Expression and Cell Identity], Alexender Diehl
:ImmPort Science Group
April 3, 2014
:'''[http://ncorwiki.buffalo.edu/index.php/Ontology_and_the_Future_of_Laboratory_Information Ontology and the Future of Laboratory Information], David Parrish (sampleminded.com)
:Buffalo CTRC
==Powerpoint Presentations==
Barry Smith, [http://ncor.buffalo.edu/2013/Immunology/Slides/Discoverability.pptx Strategies to Enhance Discoverability of Clinical Trial Data]