Difference between revisions of "Informatics"

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'''Informatics''' is the management of information.
'''Informatics''' is the management of information. [[Pathologist]]s, unfortunately, mostly have poor tools for this job.   
 
Pathologists, unfortunately, only have poor tools for this job.   
 
The two main pathology information systems (''[[Softpath]]'' and ''[[CoPath]]'') look like they are out of the early 1990s.


==Software in use at pathology departments==
==Software in use at pathology departments==
===Information systems===
===Information systems===
*[[Softpath]].  
*[[Softpath]].  
*[[CoPath]] - considered state-of-the-art... good only by comparison.
*[[CoPath]].
*[[MEDITECH]].
*[[MEDITECH]].
*[[Millennium]].
*Nexus pas.net.
*[[VANTAGE]].


===Dictation===
===Dictation===
*[[Dragon]].
*[[Dragon]].
*[[Voicebrook]].


===Content management===
===Content management===
*[[Paradigm]].
*[[Paradigm]].
===Biobanking management===
* Centraxx.
===Image analysis===
* Cytomine - under an  ''Apache license''.<ref>URL: [http://www.cytomine.be/ http://www.cytomine.be/]. Accessed on: 20 April 2016.</ref><ref name=pmid26755625>{{Cite journal  | last1 = Marée | first1 = R. | last2 = Rollus | first2 = L. | last3 = Stévens | first3 = B. | last4 = Hoyoux | first4 = R. | last5 = Louppe | first5 = G. | last6 = Vandaele | first6 = R. | last7 = Begon | first7 = JM. | last8 = Kainz | first8 = P. | last9 = Geurts | first9 = P. | title = Collaborative analysis of multi-gigapixel imaging data using Cytomine. | journal = Bioinformatics | volume =  | issue =  | pages =  | month = Jan | year = 2016 | doi = 10.1093/bioinformatics/btw013 | PMID = 26755625 }}</ref>


==Pathology wikis==
==Pathology wikis==
{{Main|Pathology wikis}}
{{Main|Pathology wikis}}
*Wiki use for the dissemination of pathology knowledge is increasing.
*Wiki use for the dissemination of pathology knowledge is increasing.
*In the general sphere, [[Wikipedia]] is dominating a will probably continue to do so.<ref name=pmid21282098>{{Cite journal  | last1 = Heilman | first1 = JM. | last2 = Kemmann | first2 = E. | last3 = Bonert | first3 = M. | last4 = Chatterjee | first4 = A. | last5 = Ragar | first5 = B. | last6 = Beards | first6 = GM. | last7 = Iberri | first7 = DJ. | last8 = Harvey | first8 = M. | last9 = Thomas | first9 = B. | title = Wikipedia: a key tool for global public health promotion. | journal = J Med Internet Res | volume = 13 | issue = 1 | pages = e14 | month =  | year = 2011 | doi = 10.2196/jmir.1589 | PMID = 21282098 }}</ref>
*In the general sphere, [[Wikipedia]] is dominating and will probably continue to do so.<ref name=pmid21282098>{{Cite journal  | last1 = Heilman | first1 = JM. | last2 = Kemmann | first2 = E. | last3 = Bonert | first3 = M. | last4 = Chatterjee | first4 = A. | last5 = Ragar | first5 = B. | last6 = Beards | first6 = GM. | last7 = Iberri | first7 = DJ. | last8 = Harvey | first8 = M. | last9 = Thomas | first9 = B. | title = Wikipedia: a key tool for global public health promotion. | journal = J Med Internet Res | volume = 13 | issue = 1 | pages = e14 | month =  | year = 2011 | doi = 10.2196/jmir.1589 | PMID = 21282098 }}</ref>


==Open source==
==Open source==
Open source in pathology appears to be some way off.  One paper,<ref name=pmid15563662>{{cite journal |author=Rubin A |title=An open pathology computer system |journal=J. Clin. Pathol. |volume=57 |issue=12 |pages=1252–3 |year=2004 |month=December |pmid=15563662 |pmc=1770514 |doi=10.1136/jcp.2004.020826 |url=}}</ref> gives me a bit of hope -- though I think this is a voice in the wilderness.   
Open source in pathology appears to be some way off.  One opinion paper<ref name=pmid15563662>{{cite journal |author=Rubin A |title=An open pathology computer system |journal=J. Clin. Pathol. |volume=57 |issue=12 |pages=1252–3 |year=2004 |month=December |pmid=15563662 |pmc=1770514 |doi=10.1136/jcp.2004.020826 |url=}}</ref> addresses this issue.   


The radiologists are more on the ball here, e.g. [http://www.mii.ucla.edu/opensourcepacs-download-2/ UCLA's OpenSourcePACS].<ref name=pmid17249408>{{Cite journal  | last1 = Bui | first1 = AA. | last2 = Morioka | first2 = C. | last3 = Dionisio | first3 = JD. | last4 = Johnson | first4 = DB. | last5 = Sinha | first5 = U. | last6 = Ardekani | first6 = S. | last7 = Taira | first7 = RK. | last8 = Aberle | first8 = DR. | last9 = El-Saden | first9 = S. | title = OpenSourcePACS: an extensible infrastructure for medical image management. | journal = IEEE Trans Inf Technol Biomed | volume = 11 | issue = 1 | pages = 94-109 | month = Jan | year = 2007 | doi =  | PMID = 17249408 }}</ref>  A few institutions (mostly American) are coming to understand this and have formed the [http://www.opendp.org/ Open Digital Pathology Consortium].
The radiologists are more on the ball here, e.g. [http://www.mii.ucla.edu/opensourcepacs-download-2/ UCLA's OpenSourcePACS].<ref name=pmid17249408>{{Cite journal  | last1 = Bui | first1 = AA. | last2 = Morioka | first2 = C. | last3 = Dionisio | first3 = JD. | last4 = Johnson | first4 = DB. | last5 = Sinha | first5 = U. | last6 = Ardekani | first6 = S. | last7 = Taira | first7 = RK. | last8 = Aberle | first8 = DR. | last9 = El-Saden | first9 = S. | title = OpenSourcePACS: an extensible infrastructure for medical image management. | journal = IEEE Trans Inf Technol Biomed | volume = 11 | issue = 1 | pages = 94-109 | month = Jan | year = 2007 | doi =  | PMID = 17249408 }}</ref>   
 
A few institutions (mostly American) are coming to understand this and have formed the [http://www.opendp.org/ Open Digital Pathology Consortium (opendp.org)]. There is also an [http://openslide.org/ open slide project (openslide.org)].


==Virtual slides==
==Virtual slides==
*There is a push for an open virtual slide format.
*There is a push for an open virtual slide format.
*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref>
*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref>
==Health informatics directory==
*The University of Freiburg put together a list in 2010.<ref>URL: [http://hiww.org/ca.html
http://hiww.org/ca.html]. Accessed on: November 8, 2014.</ref>


==See also==
==See also==
*[[Quality]].
*[[Quality]].
*[[Digital pathology]].
*[[Digital pathology]].
*[[Journal of Pathology Informatics]].


==References==
==References==
{{reflist|1}}
{{reflist|2}}
 
==External links==
*[http://pathologyinformatics.org/ Association of Pathology Informatics (pathologyinformatics.org)].


[[Category:Informatics]]
[[Category:Informatics]]

Revision as of 14:10, 20 April 2016

Informatics is the management of information. Pathologists, unfortunately, mostly have poor tools for this job.

Software in use at pathology departments

Information systems

Dictation

Content management

Biobanking management

  • Centraxx.

Image analysis

  • Cytomine - under an Apache license.[1][2]

Pathology wikis

  • Wiki use for the dissemination of pathology knowledge is increasing.
  • In the general sphere, Wikipedia is dominating and will probably continue to do so.[3]

Open source

Open source in pathology appears to be some way off. One opinion paper[4] addresses this issue.

The radiologists are more on the ball here, e.g. UCLA's OpenSourcePACS.[5]

A few institutions (mostly American) are coming to understand this and have formed the Open Digital Pathology Consortium (opendp.org). There is also an open slide project (openslide.org).

Virtual slides

  • There is a push for an open virtual slide format.
  • A free C library exists to read whole-slide images.[6]

Health informatics directory

  • The University of Freiburg put together a list in 2010.[7]

See also

References

  1. URL: http://www.cytomine.be/. Accessed on: 20 April 2016.
  2. Marée, R.; Rollus, L.; Stévens, B.; Hoyoux, R.; Louppe, G.; Vandaele, R.; Begon, JM.; Kainz, P. et al. (Jan 2016). "Collaborative analysis of multi-gigapixel imaging data using Cytomine.". Bioinformatics. doi:10.1093/bioinformatics/btw013. PMID 26755625.
  3. Heilman, JM.; Kemmann, E.; Bonert, M.; Chatterjee, A.; Ragar, B.; Beards, GM.; Iberri, DJ.; Harvey, M. et al. (2011). "Wikipedia: a key tool for global public health promotion.". J Med Internet Res 13 (1): e14. doi:10.2196/jmir.1589. PMID 21282098.
  4. Rubin A (December 2004). "An open pathology computer system". J. Clin. Pathol. 57 (12): 1252–3. doi:10.1136/jcp.2004.020826. PMC 1770514. PMID 15563662. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1770514/.
  5. Bui, AA.; Morioka, C.; Dionisio, JD.; Johnson, DB.; Sinha, U.; Ardekani, S.; Taira, RK.; Aberle, DR. et al. (Jan 2007). "OpenSourcePACS: an extensible infrastructure for medical image management.". IEEE Trans Inf Technol Biomed 11 (1): 94-109. PMID 17249408.
  6. URL: http://openslide.org/. Accessed on: 3 May 2013.
  7. URL: [http://hiww.org/ca.html http://hiww.org/ca.html]. Accessed on: November 8, 2014.

External links