User Tools

Site Tools


regsys

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
regsys [2013/02/27 09:10]
rkiss
regsys [2013/10/19 13:36] (current)
rkiss [Process outline]
Line 2: Line 2:
  
 The mcule database is curated by **MAC (Mcule Advanced Curation)** that involves a rigorous molecule registration system based on more than 80 structural checks, standardization, preparation and correction steps. MAC guarantees high quality search results and avoids common errors arising from mis-drawn and incorrect structures that can critically affect the quality of computational calculations and the efficiency of experimental results. The mcule database is curated by **MAC (Mcule Advanced Curation)** that involves a rigorous molecule registration system based on more than 80 structural checks, standardization, preparation and correction steps. MAC guarantees high quality search results and avoids common errors arising from mis-drawn and incorrect structures that can critically affect the quality of computational calculations and the efficiency of experimental results.
 +
 +**Key features of MAC:** high level data curation, stereochemical standardization, robust novelty check and isomer detection, correct handling of salts & organometallics
 +
 +Continue reading for more information about MAC, or check our presentations from the 244th National Meeting of American Chemical Society:
 +
 +[[http://mcule-blog.s3.amazonaws.com/acs12/mcule_ACS12_Phi_libraries.pdf|Evaluation of data quality in currently available compound libraries (slides)]]
 +
 +[[http://mcule-blog.s3.amazonaws.com/acs12/mcule_ACS12_libraries.jpg|Evaluation of data quality in currently available compound libraries (poster)]]
 +
  
 ==== Quality is important ==== ==== Quality is important ====
Line 9: Line 18:
 The mcule structure registration system is primarily designed to correctly handle chemical structures coming from different data sources, mainly from chemical suppliers, and load the structures into the mcule database. This is a non-trivial task which requires a careful structure check and preparation procedure. To reach a high curation level, the registration system should ensure database quality in terms of structure correctness, uniqueness and reliability as well as maintain a high level of data standardization. The mcule structure registration system is primarily designed to correctly handle chemical structures coming from different data sources, mainly from chemical suppliers, and load the structures into the mcule database. This is a non-trivial task which requires a careful structure check and preparation procedure. To reach a high curation level, the registration system should ensure database quality in terms of structure correctness, uniqueness and reliability as well as maintain a high level of data standardization.
  
-**All molecules with an MCULE ID have been processed by MAC**. User uploaded molecules are not processed by MAC by default. We will enable this option in future. +**All molecules with an MCULE ID have been processed by MAC**. User uploaded molecules are not processed by MAC by default. We plan to enable this option in future.
- +
-**Key features:** high level data curation, stereochemical standardization, robust novelty check and isomer detection, correct handling of salts & organometallics+
  
 ==== Registration challenges ==== ==== Registration challenges ====
Line 50: Line 57:
 ===== Process outline ===== ===== Process outline =====
  
-The whole registration process can be divided into seven different stages. It begins with the revision of stereo configurations, structure check/preparation steps (stage A, B) followed by component separation (stage C). Thereafter component uniqueness is checked and mcule IDs are assigned (stage D, E). This is performed with or without considering tautomerism and protonation, resulting the assignment of tautomer and protonation state independent [[mculeid|compound identifiers]] (stage D) as well as tautomer and protonation state dependent [[mculeid|structure identifiers]] (stage E). Finally, based on component identity, multicomponent entries are also registered at both the tautomer and protonation state independent (stage F) and dependent levels (stage G).+The whole registration process can be divided into seven different stages. It begins with the revision of stereo configurations, structure check/preparation steps (stage A, B) followed by component separation (stage C). Thereafter component uniqueness is checked and mcule IDs are assigned (stage D, E). This is performed with or without considering tautomerism and protonation, resulting the assignment of tautomer and protonation state independent [[structurelevels|compound identifiers]] (stage D) as well as tautomer and protonation state dependent [[structurelevels|structure identifiers]] (stage E). Finally, based on component identity, multicomponent entries are also registered at both the tautomer and protonation state independent (stage F) and dependent levels (stage G).
  
 |Stage A |Enforcing [[stereonotations|standard stereo representation]]; non-standard stereo notations are changed, unreliable part of stereo configurations is removed (after consulting with chemical supplier) | |Stage A |Enforcing [[stereonotations|standard stereo representation]]; non-standard stereo notations are changed, unreliable part of stereo configurations is removed (after consulting with chemical supplier) |
Line 59: Line 66:
  
 As a result, input entries as well as their components are registered at two levels: tautomer and protonation state independent [[structurelevels|compound level]] with tautomer detection and tautomer and protonation state dependent [[structurelevels|structure level]] without tautomer detection. As a result, input entries as well as their components are registered at two levels: tautomer and protonation state independent [[structurelevels|compound level]] with tautomer detection and tautomer and protonation state dependent [[structurelevels|structure level]] without tautomer detection.
- 
 ===== Registration process ===== ===== Registration process =====
  
Line 185: Line 191:
 In most cases the system is also capable of identifying the main components, which can serve as the input set for virtual screens. In most cases the system is also capable of identifying the main components, which can serve as the input set for virtual screens.
  
-You can see below the index page of compound [[https://mcule.com/MCULE-3198812899|MCULE-3198812899]]. This is a maleic and/or fumaric acid salt+You can see below the index page of compound [[https://mcule.com/MCULE-3198812899/|MCULE-3198812899]]. This is a maleic and/or fumaric acid salt
 (uncertainty is marked by crossed double bond). Counter ions are marked, and component multiplicities are assigned correctly by the system. (uncertainty is marked by crossed double bond). Counter ions are marked, and component multiplicities are assigned correctly by the system.
  
 {{:regsys:reg_sys_12.png|}} {{:regsys:reg_sys_12.png|}}
regsys.1361952607.txt.gz · Last modified: 2013/02/27 09:10 by rkiss