Difference between revisions of "Cancer informatics"

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'''Cancer informatics''' is a multidisciplinary field of science that "deals with the resources, devices, and methods required to optimize the acquisition, storage, retrieval, and use of [[information]] in cancer" research and treatment.<ref name="NCRACancerInfo">{{cite web |url=http://www.ncra-usa.org/i4a/pages/index.cfm?pageid=3934 |title=Cancer Informatics |publisher=National Cancer Registrars Association |accessdate=19 June 2014}}</ref> Like many other fields of science, researchers in cancer biology have seen a dramatic increase in the amount of clinical and research data, in particular with genomic and molecular cancer data. While this data can benefit researchers' understanding of cancer behavior and development of better therapies, new and improved data management and analysis tools are needed. Cancer informatics attempts to provide those tools "that interconnect research, clinical activities, and data in an organized and efficient manner, with as broad a database as possible."<ref name="NassInfo">{{cite book |url=http://books.google.com/books?id=qWuJAco_5R8C&pg=PA7 |chapter=Chapter 2: Overview of the Cancer Informatics Landscape |title=Informatics Needs and Challenges in Cancer Research: Workshop Summary |author=Nass, Sharyl J.; Wizemann, Theresa (eds.) |publisher=National Academies Press |pages=7–30 |year=2012 |isbn=9780309259484 |accessdate=19 June 2014}}</ref> For many, the coupling of cancer informatics and other [[bioinformatics]] tools with computational modeling and statistical analysis will accelerate the goal of making cancer a more treatable if not curable disease.<ref name="OchsBio">{{cite book |url=http://books.google.com/books?id=Ej8J_BZFON4C&printsec=frontcover |chapter=Chapter 1: Biomedical Informatics for Cancer Research: Introduction |title=Biomedical Informatics for Cancer Research |authors=Ochs, Michael F.; Casagrande, John T.; Davuluri, Ramana V. |publisher=Springer |pages=3–16 |year=2010 |isbn=9781441957122 |accessdate=19 June 2014}}</ref>
[[File:In-Silico-Gene-Prioritization-by-Integrating-Multiple-Data-Sources-pone.0021137.g005.jpg|500px|right]]'''Cancer informatics''' is a multidisciplinary field of science that "deals with the resources, devices, and methods required to optimize the acquisition, storage, retrieval, and use of [[information]] in cancer" research and treatment.<ref name="NCRACancerInfo">{{cite web |url=http://www.ncra-usa.org/Education/Informatics |title=Cancer Informatics |publisher=National Cancer Registrars Association |accessdate=19 March 2020}}</ref> Like many other fields of science, researchers in cancer biology have seen a dramatic increase in the amount of clinical and research data, in particular with genomic and molecular cancer data. While this data can benefit researchers' understanding of cancer behavior and development of better therapies, new and improved [[Information management|data management]] and [[Data analysis|analysis]] tools are needed. Cancer informatics attempts to provide those tools "that interconnect research, clinical activities, and data in an organized and efficient manner, with as broad a database as possible."<ref name="NassInfo">{{cite book |url=https://books.google.com/books?id=qWuJAco_5R8C&pg=PA7 |chapter=Chapter 2: Overview of the Cancer Informatics Landscape |title=Informatics Needs and Challenges in Cancer Research: Workshop Summary |author=Nass, S.J.; Wizemann, T. (eds.) |publisher=National Academies Press |pages=7–30 |year=2012 |isbn=9780309259484 |accessdate=19 March 2020}}</ref> For many, the coupling of cancer informatics and other [[bioinformatics]] tools with computational modeling and statistical analysis will accelerate the goal of making cancer a more treatable if not curable disease.<ref name="OchsBio">{{cite book |url=https://books.google.com/books?id=Ej8J_BZFON4C&printsec=frontcover |chapter=Chapter 1: Biomedical Informatics for Cancer Research: Introduction |title=Biomedical Informatics for Cancer Research |authors=Ochs, M.F.; Casagrande, J.T.; Davuluri, R.V. |publisher=Springer |pages=3–16 |year=2010 |isbn=9781441957122 |accessdate=19 March 2020}}</ref>
 


==Application==
==Application==
Cancer informatics can help tackle problems and tasks such as the following<ref name="OchsBio" />:
Cancer informatics can help tackle problems and tasks such as the following<ref name="OchsBio" /><ref name="SalemMachine">{{cite book |url=https://link.springer.com/chapter/10.1007%2F978-3-319-00029-9_1 |chapter=Chapter 1: Machine Learning Applications in Cancer Informatics |title=Advances in Intelligent Analysis of Medical Data and Decision Support Systems |series=Studies in Computational Intelligence |author=Salem, A.-B.M. |publisher=Springer |pages=1–14 |year=2013 |isbn=9783319000282 |accessdate=19 March 2020}}</ref>:


* the development of computational diagnosis, prognosis, and predictive models
* the development of computational diagnosis, prognosis, and predictive models
* the development of standards for the entry, annotation, and sharing of clinical cancer data
* the development of standards for the entry, annotation, and sharing of clinical cancer data
* the management and distribution of annotated molecular data for further research
* the management and distribution of annotated molecular data for further research
* the analysis of an individual tumor to determine it molecular phenotype
* the analysis of an individual tumor to determine its molecular phenotype
* the development of a treatment plan based on a tumor's molecular phenotype
* the development of a treatment plan based on a tumor's molecular phenotype
* the tracking of the aberrations that drive a particular cancer's growth
* the tracking of the aberrations that drive a particular cancer's growth


==Cancer informatics around the world==
===In the United States===
In the U.S., the field of cancer informatics became much more noticeable with the late 1990s push by the [[National Cancer Institute]]'s (NCI's) director Richard D. Klausner to create "a Cancer Informatics Infrastructure (CII) to enable the cancer research enterprise and to link it to the delivery of cancer care."<ref name="SilvaCI">{{cite book |url=https://books.google.com/books?id=DhNSheaOeDEC |chapter=Foreward |title=Cancer Informatics: Essential Technologies for Clinical Trials |series=Health Informatics |author=Klausner, R.D.; Silva, J.S. (ed.) |pages=vii–x |year=2002 |isbn=9781461265474 |accessdate=19 March 2020}}</ref> Klausner saw clinical trials as one of the key components of cancer research. Given their value to researchers, he recognized clinical trials would require improved efficiency and openness as well as a new way of openly linking interested parties to the associated trial data via an information management system. Such a system would need to not only manage clinical trial data but also provide tools to turn such data into meaningful information.<ref name="SilvaCI" />
In the spring of 2004, the NCI began funding the [[caBIG]] initiative, which sought to connect U.S. biomedical cancer researchers using technology known as grid computing. The program, led by the Center for Bioinformatics and Information Technology (CBIIT), began with a three-year pilot phase. The pilot phase concluded in March 2007, and 56 NCI-designated cancer centers started a trial.<ref name="AssImpcaBIG">{{cite web |url=https://deainfo.nci.nih.gov/advisory/bsa/archive/bsa0311/caBIGfinalReport.pdf |format=PDF |title=An Assessment of the Impact of the NCI CaBIG |publisher=National Cancer Institute |date=March 2011 |accessdate=19 March 2020}}</ref> The project was furthered still with the development of software and standards to support project goals. By 2011, the NCI concluded the original goals of the caBIG initiative were worthy of pursuing, but the program had become bloated and off-course. This led to the April 2012 creation of a new National Cancer Informatics Program (NCIP) that would act as the spiritual successor of caBIG, integrating some of its informatics programs and ceasing development on others.<ref name="CDISCcaBIG">{{cite web |url=https://www.cdisc.org/where-cabig-going%3F |title=Where is caBIG Going? |publisher=CDISC |date=09 July 2012 |accessdate=19 March 2020}}</ref><ref name="NCIPCreationArch">{{cite web |url=https://cabig.nci.nih.gov/NCIP-launch-meeting |archiveurl=http://web.archive.org/web/20130216034021/https://cabig.nci.nih.gov/NCIP-launch-meeting |title=National Cancer Informatics Program Launch Meeting |author=Komatsoulis, G.A. |publisher=National Cancer Institute |date=April 2012 |archivedate=16 February 2013 |accessdate=08 May 2013}}</ref> {{As of |March 2020}} the NCIP was still being enacted, funding and developing projects related to cancer genomics data management, creating a software sharing hub, and releasing code under the open-source model.
===In other parts of the world===
In 2008, Greek bioinformatician Manolis Tsiknakis discussed the state of cancer informatics in Europe at the 8th IEEE International Conference on BioInformatics and BioEngineering.<ref name="ManoCIEurope">{{cite journal |title=The European cancer informatics landscape: Challenges for the biomedical informatics community |journal=8th IEEE International Conference on BioInformatics and BioEngineering, 2008 |author=Tsiknakis, M. |pages=1–7 |year=2008 |doi=10.1109/BIBE.2008.4696649}}</ref> He noted developments such as the Advancing Clinico Genomic Trials on Cancer (ACGT) program, which was originally envisaged as "a unified technological infrastructure which will facilitate the seamless and secure access and analysis of multi-level clinical and genomic data enriched with high-performing knowledge discovery operations and services in support of multi-centric, post-genomic clinical trials."<ref name="ManoCIEurope" /> (The ACGT program was eventually halted at the end of July 2010.<ref name="ACGTCordis">{{cite web |url=https://cordis.europa.eu/project/id/026996 |title=Advancing Clinico-Genomic Trials on Cancer: Open Grid Services for Improving Medical Knowledge Discovery |publisher=Publications Office of the European Union |work=CORDIS |date=07 October 2014 |accessdate=19 March 2020}}</ref><ref name="ACGTArch1">{{cite web |url=http://eu-acgt.org/ |archiveurl=https://web.archive.org/web/20110107201922/http://eu-acgt.org/ |title=ACGT: Advancing Clinico Genomic Trials |publisher=European Commission Information Society and Media |archivedate=07 January 2011 |accessdate=12 January 2015}}</ref>) Tsiknakis also referenced the development of the multi-disciplinary myGrid project in the United Kingdom, a funded effort to help others with the challenges of eScience until at least 2016.<ref name="myGridAbout">{{cite web |url=http://www.mygrid.org.uk/about-us/ |title=myGrid: About us |publisher=myGrid |accessdate=19 March 2020}}</ref>
The United States' National Cancer Institute has also played a role in broadening cancer informatics beyond the U.S. Through its Request for Proposals for Pilot Collaborations with Low- and Mid-Income Countries (LMICs) program, the NCI has funded the development of cancer informatics infrastructure in countries like El Salvador and Honduras.<ref name="CGHAwards">{{cite web |url=https://www.cancer.gov/about-nci/organization/cgh/blog/2014/2013-cgh-awardees |title=2013 Awardees: Request for Proposals for Pilot Collaborations with Low- and Mid-Income Countries (LMICs) in Global Cancer Research or Global Health Research at NCI-Designated Cancer Centers |author=Trimble, T. |publisher=National Cancer Institute |date=23 June 2014 |accessdate=19 March 2020}}</ref>


==Informatics==
==Cancer informatics projects, organizations, and events==
Examples of cancer informatics projects, organizations, and events include:


* [https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga Cancer Genome Atlas]: an NCI-funded initiative "to generate comprehensive, multi-dimensional maps of the key genomic changes in major types and subtypes of cancer"
* [http://www.ci4cc.org/about Cancer Informatics for Cancer Centers] (CI4CC): a non-profit "intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world, but with a special emphasis on all 70 NCI-funded cancer centers"
* [https://www.cancerlinq.org/ CancerLinQ]: driven by the American Society of Clinical Oncology, this program aims to assemble "vast amounts of usable, searchable, real-world cancer information into a powerful database"
* [https://esciencelab.org.uk/ eScience Lab]: formerly [http://www.mygrid.org.uk/about-us/ myGrid], a U.K. initiative to develop informatics software for scientists, including cancer researchers
* [https://datascience.cancer.gov/resources/ITCR-tools Informatics Technology for Cancer Research (ITCR) Tools]: an NCI initiative to manage and expand on the cancer informatics tools and infrastructure of the NCI's extramural divisions
* [https://the-ici-fund.org/events/summit-2019 Innovation in Cancer Informatics Summit]: a conference on cancer informatics innovation


==External links==
==External links==
* [http://www.la-press.com/journal-cancer-informatics-j10 Cancer Informatics] journal
* [https://us.sagepub.com/en-us/nam/cancer-informatics/journal202627 Cancer Informatics] journal
* [http://www.cancerinformaticssummit.com/ Cancer Informatics Summit]
* [https://ascopubs.org/journal/cci JCO Clinical Cancer Informatics] journal
* [http://www.asco.org/quality-guidelines/cancerlinq CancerLinQ]
* [http://cbiit.nci.nih.gov/ncip National Cancer Informatics Program] homepage
* [https://github.com/ncip National Cancer Informatics Program] at GitHub
* [https://github.com/ncip National Cancer Informatics Program] at GitHub


==References==
==References==
<references/>
{{Reflist|colwidth=30em}}


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<!---Place all category tags here-->
[[Category:Informatics]]
[[Category:Informatics]]

Revision as of 17:59, 20 March 2020

In-Silico-Gene-Prioritization-by-Integrating-Multiple-Data-Sources-pone.0021137.g005.jpg

Cancer informatics is a multidisciplinary field of science that "deals with the resources, devices, and methods required to optimize the acquisition, storage, retrieval, and use of information in cancer" research and treatment.[1] Like many other fields of science, researchers in cancer biology have seen a dramatic increase in the amount of clinical and research data, in particular with genomic and molecular cancer data. While this data can benefit researchers' understanding of cancer behavior and development of better therapies, new and improved data management and analysis tools are needed. Cancer informatics attempts to provide those tools "that interconnect research, clinical activities, and data in an organized and efficient manner, with as broad a database as possible."[2] For many, the coupling of cancer informatics and other bioinformatics tools with computational modeling and statistical analysis will accelerate the goal of making cancer a more treatable if not curable disease.[3]

Application

Cancer informatics can help tackle problems and tasks such as the following[3][4]:

  • the development of computational diagnosis, prognosis, and predictive models
  • the development of standards for the entry, annotation, and sharing of clinical cancer data
  • the management and distribution of annotated molecular data for further research
  • the analysis of an individual tumor to determine its molecular phenotype
  • the development of a treatment plan based on a tumor's molecular phenotype
  • the tracking of the aberrations that drive a particular cancer's growth

Cancer informatics around the world

In the United States

In the U.S., the field of cancer informatics became much more noticeable with the late 1990s push by the National Cancer Institute's (NCI's) director Richard D. Klausner to create "a Cancer Informatics Infrastructure (CII) to enable the cancer research enterprise and to link it to the delivery of cancer care."[5] Klausner saw clinical trials as one of the key components of cancer research. Given their value to researchers, he recognized clinical trials would require improved efficiency and openness as well as a new way of openly linking interested parties to the associated trial data via an information management system. Such a system would need to not only manage clinical trial data but also provide tools to turn such data into meaningful information.[5]

In the spring of 2004, the NCI began funding the caBIG initiative, which sought to connect U.S. biomedical cancer researchers using technology known as grid computing. The program, led by the Center for Bioinformatics and Information Technology (CBIIT), began with a three-year pilot phase. The pilot phase concluded in March 2007, and 56 NCI-designated cancer centers started a trial.[6] The project was furthered still with the development of software and standards to support project goals. By 2011, the NCI concluded the original goals of the caBIG initiative were worthy of pursuing, but the program had become bloated and off-course. This led to the April 2012 creation of a new National Cancer Informatics Program (NCIP) that would act as the spiritual successor of caBIG, integrating some of its informatics programs and ceasing development on others.[7][8] As of March 2020 the NCIP was still being enacted, funding and developing projects related to cancer genomics data management, creating a software sharing hub, and releasing code under the open-source model.

In other parts of the world

In 2008, Greek bioinformatician Manolis Tsiknakis discussed the state of cancer informatics in Europe at the 8th IEEE International Conference on BioInformatics and BioEngineering.[9] He noted developments such as the Advancing Clinico Genomic Trials on Cancer (ACGT) program, which was originally envisaged as "a unified technological infrastructure which will facilitate the seamless and secure access and analysis of multi-level clinical and genomic data enriched with high-performing knowledge discovery operations and services in support of multi-centric, post-genomic clinical trials."[9] (The ACGT program was eventually halted at the end of July 2010.[10][11]) Tsiknakis also referenced the development of the multi-disciplinary myGrid project in the United Kingdom, a funded effort to help others with the challenges of eScience until at least 2016.[12]

The United States' National Cancer Institute has also played a role in broadening cancer informatics beyond the U.S. Through its Request for Proposals for Pilot Collaborations with Low- and Mid-Income Countries (LMICs) program, the NCI has funded the development of cancer informatics infrastructure in countries like El Salvador and Honduras.[13]

Cancer informatics projects, organizations, and events

Examples of cancer informatics projects, organizations, and events include:

  • Cancer Genome Atlas: an NCI-funded initiative "to generate comprehensive, multi-dimensional maps of the key genomic changes in major types and subtypes of cancer"
  • Cancer Informatics for Cancer Centers (CI4CC): a non-profit "intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world, but with a special emphasis on all 70 NCI-funded cancer centers"
  • CancerLinQ: driven by the American Society of Clinical Oncology, this program aims to assemble "vast amounts of usable, searchable, real-world cancer information into a powerful database"
  • eScience Lab: formerly myGrid, a U.K. initiative to develop informatics software for scientists, including cancer researchers
  • Informatics Technology for Cancer Research (ITCR) Tools: an NCI initiative to manage and expand on the cancer informatics tools and infrastructure of the NCI's extramural divisions
  • Innovation in Cancer Informatics Summit: a conference on cancer informatics innovation

External links

References

  1. ↑ "Cancer Informatics". National Cancer Registrars Association. http://www.ncra-usa.org/Education/Informatics. Retrieved 19 March 2020. 
  2. ↑ Nass, S.J.; Wizemann, T. (eds.) (2012). "Chapter 2: Overview of the Cancer Informatics Landscape". Informatics Needs and Challenges in Cancer Research: Workshop Summary. National Academies Press. pp. 7–30. ISBN 9780309259484. https://books.google.com/books?id=qWuJAco_5R8C&pg=PA7. Retrieved 19 March 2020. 
  3. ↑ 3.0 3.1 Ochs, M.F.; Casagrande, J.T.; Davuluri, R.V. (2010). "Chapter 1: Biomedical Informatics for Cancer Research: Introduction". Biomedical Informatics for Cancer Research. Springer. pp. 3–16. ISBN 9781441957122. https://books.google.com/books?id=Ej8J_BZFON4C&printsec=frontcover. Retrieved 19 March 2020. 
  4. ↑ Salem, A.-B.M. (2013). "Chapter 1: Machine Learning Applications in Cancer Informatics". Advances in Intelligent Analysis of Medical Data and Decision Support Systems. Studies in Computational Intelligence. Springer. pp. 1–14. ISBN 9783319000282. https://link.springer.com/chapter/10.1007%2F978-3-319-00029-9_1. Retrieved 19 March 2020. 
  5. ↑ 5.0 5.1 Klausner, R.D.; Silva, J.S. (ed.) (2002). "Foreward". Cancer Informatics: Essential Technologies for Clinical Trials. Health Informatics. pp. vii–x. ISBN 9781461265474. https://books.google.com/books?id=DhNSheaOeDEC. Retrieved 19 March 2020. 
  6. ↑ "An Assessment of the Impact of the NCI CaBIG" (PDF). National Cancer Institute. March 2011. https://deainfo.nci.nih.gov/advisory/bsa/archive/bsa0311/caBIGfinalReport.pdf. Retrieved 19 March 2020. 
  7. ↑ "Where is caBIG Going?". CDISC. 9 July 2012. https://www.cdisc.org/where-cabig-going%3F. Retrieved 19 March 2020. 
  8. ↑ Komatsoulis, G.A. (April 2012). "National Cancer Informatics Program Launch Meeting". National Cancer Institute. Archived from the original on 16 February 2013. http://web.archive.org/web/20130216034021/https://cabig.nci.nih.gov/NCIP-launch-meeting. Retrieved 08 May 2013. 
  9. ↑ 9.0 9.1 Tsiknakis, M. (2008). "The European cancer informatics landscape: Challenges for the biomedical informatics community". 8th IEEE International Conference on BioInformatics and BioEngineering, 2008: 1–7. doi:10.1109/BIBE.2008.4696649. 
  10. ↑ "Advancing Clinico-Genomic Trials on Cancer: Open Grid Services for Improving Medical Knowledge Discovery". CORDIS. Publications Office of the European Union. 7 October 2014. https://cordis.europa.eu/project/id/026996. Retrieved 19 March 2020. 
  11. ↑ "ACGT: Advancing Clinico Genomic Trials". European Commission Information Society and Media. Archived from the original on 07 January 2011. https://web.archive.org/web/20110107201922/http://eu-acgt.org/. Retrieved 12 January 2015. 
  12. ↑ "myGrid: About us". myGrid. http://www.mygrid.org.uk/about-us/. Retrieved 19 March 2020. 
  13. ↑ Trimble, T. (23 June 2014). "2013 Awardees: Request for Proposals for Pilot Collaborations with Low- and Mid-Income Countries (LMICs) in Global Cancer Research or Global Health Research at NCI-Designated Cancer Centers". National Cancer Institute. https://www.cancer.gov/about-nci/organization/cgh/blog/2014/2013-cgh-awardees. Retrieved 19 March 2020. 
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