Difference between revisions of "Scientific data management system"

From LIMSWiki
Jump to navigationJump to search
m (Reverted edits by MediaWiki spam cleanup (talk) to last revision by Shawndouglas)
m (Cleaned up citations)
Line 1: Line 1:
[[File:NIST Testing standard interfaces.jpg|right|thumb|NIST tests standard interfaces for its lab equipment. SDMSs allow labs to integrate equipment data with other types of data.]]A '''scientific data management system''' (SDMS) is a piece or package of software that acts as a document management system (DMS), capturing, cataloging, and archiving data generated by [[laboratory]] instruments ([[HPLC]], [[mass spectrometry]]) and applications ([[LIMS]], analytical applications, [[electronic laboratory notebook]]s) in a compliant manner. The SDMS also acts as a gatekeeper, serving platform-independent data to informatics applications and/or other consumers.
[[File:NIST Testing standard interfaces.jpg|right|thumb|NIST tests standard interfaces for its lab equipment. SDMSs allow labs to integrate equipment data with other types of data.]]A '''scientific data management system''' (SDMS) is software that acts as a document management system (DMS), capturing, cataloging, and archiving data generated by [[laboratory]] instruments ([[HPLC]], [[mass spectrometry]]) and applications ([[LIMS]], analytical applications, [[electronic laboratory notebook]]s) in a compliant manner. The SDMS also acts as a gatekeeper, serving platform-independent data to informatics applications and/or other consumers.


As with many other [[laboratory informatics]] tools, the lines between a [[LIMS]], [[ELN]], and an SDMS are at times blurred. However, there are some essential qualities that an SDMS owns that distinguishes it from other informatics systems:
As with many other [[laboratory informatics]] tools, the lines between a [[LIMS]], [[ELN]], and an SDMS are at times blurred. However, there are some essential qualities that an SDMS owns that distinguishes it from other informatics systems:


1. While a LIMS has traditionally been built to handle structured, mostly homogeneous data, a SDMS (and systems like it) is built to handle unstructured, mostly heterogeneous data.<ref>{{cite web|url=http://www.scientificcomputing.com/considerations-for-management.aspx |author=Elliott, Michael H.|title=Considerations for Management of Laboratory Data |publisher=Scientific Computing |date=15 September 2009 |accessdate=04 May 2011}}</ref>
1. While a LIMS has traditionally been built to handle structured, mostly homogeneous data, a SDMS (and systems like it) is built to handle unstructured, mostly heterogeneous data.<ref name="ElliottConsider03">{{cite web |url=https://www.scientificcomputing.com/article/2003/10/considerations-management-laboratory-data |title=Considerations for Management of Laboratory Data |author=Elliott, M.H. |work=Scientific Computing |publisher=Advantage Business Media |date=31 October 2003 |accessdate=29 September 2017}}</ref>


2. A SDMS typically acts as a seamless "wrapper" for other data systems like LIMS and ELN in the laboratory, though sometimes the SDMS software is readily apparent.
2. A SDMS typically acts as a seamless "wrapper" for other data systems like LIMS and ELN in the laboratory, though sometimes the SDMS software is readily apparent.


3. A SDMS is designed primarily for data consolidation, knowledge management, and knowledge asset realization. <ref>Wood, Simon (2007). [http://www.starlims.com/AL-Wood-Reprint-9-07.pdf "Comprehensive Laboratory Informatics: A Multilayer Approach"], pp. 3.</ref>
3. A SDMS is designed primarily for data consolidation, knowledge management, and knowledge asset realization.<ref name="WoodComp07">{{cite web |url=https://www.it.uu.se/edu/course/homepage/lims/vt12/ComprehensiveLaboratoryInformatics.pdf |archiveurl=https://web.archive.org/web/20170825181932/https://www.it.uu.se/edu/course/homepage/lims/vt12/ComprehensiveLaboratoryInformatics.pdf |format=PDF |title=Comprehensive Laboratory Informatics: A Multilayer Approach |author=Wood, S. |work=American Laboratory |page=1 |date=September 2007 |archivedate=25 August 2017}}</ref>


An SDMS can be seen as one potential solution for handling unstructured data, which can make up nearly 75 percent of a research and development unit's data.<ref name="SciComp1">{{cite web|url=http://www.scientificcomputing.com/tomorrows-successful-research.aspx |author=Deutsch, Scott |title=Tomorrow’s Successful Research Organizations Face a Critical Challenge |publisher=Scientific Computing |date=30 July 2008 |accessdate=04 May 2011}}</ref> This includes PDF files, images, instrument data, spreadsheets, and other forms of data rendered in many environments in the laboratory. Traditional SDMSs have focused on acting as a nearly invisible blanket or wrapper that integrate [[information]] from corporate offices (SOPs, safety documents, etc.) with data from lab devices and other data management tools, all to be indexed and searchable from a central database. An SDMS also must be focused on increasing research productivity without sacrificing data sharing and collaboration efforts.<ref name="SciComp1" />
An SDMS can be seen as one potential solution for handling unstructured data, which can make up nearly 75 percent of a research and development unit's data.<ref name="SciComp1">{{cite web |url=https://www.scientificcomputing.com/article/2006/12/tomorrow%E2%80%99s-successful-research-organizations-face-critical-challenge |author=Deutsch, S. |title=Tomorrow’s Successful Research Organizations Face a Critical Challenge |work=Scientific Computing |publisher=Advantage Business Media |date=31 December 2006 |accessdate=29 September 2017}}</ref> This includes PDF files, images, instrument data, spreadsheets, and other forms of data rendered in many environments in the laboratory. Traditional SDMSs have focused on acting as a nearly invisible blanket or wrapper that integrate [[information]] from corporate offices (standard operating procedures, safety documents, etc.) with data from lab devices and other data management tools, all to be indexed and searchable from a central database. An SDMS also must be focused on increasing research productivity without sacrificing data sharing and collaboration efforts.<ref name="SciComp1" />


Some of the things a standard SDMS may be asked to do include, but are not limited to<ref name="SDMArch">{{cite web |url=http://personal.cscs.ch/~mvalle/sdm/scientific-data-management.html |archiveurl=http://web.archive.org/web/20120306015034/http://personal.cscs.ch/~mvalle/sdm/scientific-data-management.html |author=Valle, Mario |title=Scientific Data Management |publisher=Swiss National Supercomputing Center |archivedate=06 March 2012 |accessdate=05 March 2013}}</ref><ref>Heyward, Joseph E. II (2009). [https://scholarworks.iupui.edu/handle/1805/2000 "Selection of a Scientific Data Management System (SDMS) Based on User Requirements"], pp. 1–5 (PDF).</ref>:
Some of the things a standard SDMS may be asked to do include, but are not limited to<ref name="SDMArch">{{cite web |url=http://personal.cscs.ch/~mvalle/sdm/scientific-data-management.html |archiveurl=http://web.archive.org/web/20120306015034/http://personal.cscs.ch/~mvalle/sdm/scientific-data-management.html |author=Valle, Mario |title=Scientific Data Management |publisher=Swiss National Supercomputing Center |archivedate=06 March 2012 |accessdate=05 March 2013}}</ref><ref name="HetwardSelect09">{{cite web |url=https://scholarworks.iupui.edu/handle/1805/2000 |title=Selection of a Scientific Data Management System (SDMS) Based on User Requirements |author=Heyward, J.E. II |publisher=Indiana University-Purdue University Indianapolis |date=05 November 2009 |pages=5 |accessdate=29 September 2017}}</ref>:


* retrieve worklists from LIMS and convert them to sequence files
* retrieve worklists from LIMS and convert them to sequence files

Revision as of 17:25, 29 September 2017

NIST tests standard interfaces for its lab equipment. SDMSs allow labs to integrate equipment data with other types of data.

A scientific data management system (SDMS) is software that acts as a document management system (DMS), capturing, cataloging, and archiving data generated by laboratory instruments (HPLC, mass spectrometry) and applications (LIMS, analytical applications, electronic laboratory notebooks) in a compliant manner. The SDMS also acts as a gatekeeper, serving platform-independent data to informatics applications and/or other consumers.

As with many other laboratory informatics tools, the lines between a LIMS, ELN, and an SDMS are at times blurred. However, there are some essential qualities that an SDMS owns that distinguishes it from other informatics systems:

1. While a LIMS has traditionally been built to handle structured, mostly homogeneous data, a SDMS (and systems like it) is built to handle unstructured, mostly heterogeneous data.[1]

2. A SDMS typically acts as a seamless "wrapper" for other data systems like LIMS and ELN in the laboratory, though sometimes the SDMS software is readily apparent.

3. A SDMS is designed primarily for data consolidation, knowledge management, and knowledge asset realization.[2]

An SDMS can be seen as one potential solution for handling unstructured data, which can make up nearly 75 percent of a research and development unit's data.[3] This includes PDF files, images, instrument data, spreadsheets, and other forms of data rendered in many environments in the laboratory. Traditional SDMSs have focused on acting as a nearly invisible blanket or wrapper that integrate information from corporate offices (standard operating procedures, safety documents, etc.) with data from lab devices and other data management tools, all to be indexed and searchable from a central database. An SDMS also must be focused on increasing research productivity without sacrificing data sharing and collaboration efforts.[3]

Some of the things a standard SDMS may be asked to do include, but are not limited to[4][5]:

  • retrieve worklists from LIMS and convert them to sequence files
  • interact real-time with simple and complex laboratory instruments
  • analyze and create reports on laboratory instrument functions
  • perform complex calculations and comparisons of two different sample groups
  • monitor environmental conditions and react when base operating parameters are out of range
  • act as an operational database that allows selective importation/exportation of ELN data
  • manage workflows based on data imported into the SDMS
  • validate other computer systems and software in the laboratory

SDMS vendors

See the SDMS vendor page for a list of SDMS vendors past and present.

References

  1. ↑ Elliott, M.H. (31 October 2003). "Considerations for Management of Laboratory Data". Scientific Computing. Advantage Business Media. https://www.scientificcomputing.com/article/2003/10/considerations-management-laboratory-data. Retrieved 29 September 2017. 
  2. ↑ Wood, S. (September 2007). "Comprehensive Laboratory Informatics: A Multilayer Approach" (PDF). American Laboratory. p. 1. Archived from the original on 25 August 2017. https://web.archive.org/web/20170825181932/https://www.it.uu.se/edu/course/homepage/lims/vt12/ComprehensiveLaboratoryInformatics.pdf. 
  3. ↑ 3.0 3.1 Deutsch, S. (31 December 2006). "Tomorrow’s Successful Research Organizations Face a Critical Challenge". Scientific Computing. Advantage Business Media. https://www.scientificcomputing.com/article/2006/12/tomorrow%E2%80%99s-successful-research-organizations-face-critical-challenge. Retrieved 29 September 2017. 
  4. ↑ Valle, Mario. "Scientific Data Management". Swiss National Supercomputing Center. Archived from the original on 06 March 2012. http://web.archive.org/web/20120306015034/http://personal.cscs.ch/~mvalle/sdm/scientific-data-management.html. Retrieved 05 March 2013. 
  5. ↑ Heyward, J.E. II (5 November 2009). "Selection of a Scientific Data Management System (SDMS) Based on User Requirements". Indiana University-Purdue University Indianapolis. pp. 5. https://scholarworks.iupui.edu/handle/1805/2000. Retrieved 29 September 2017. 
Retrieved from "https://www.limswiki.org/index.php?title=Scientific_data_management_system&oldid=31776"