PMID- 18236171
OWN - NLM
STAT- MEDLINE
DCOM- 20080605
LR  - 20211020
IS  - 1345-711X (Print)
IS  - 1345-711X (Linking)
VI  - 8
IP  - 4
DP  - 2007 Dec
TI  - A graphical approach to tracking and reporting target status in structural 
      genomics.
PG  - 209-16
LID - 10.1007/s10969-007-9037-0 [doi]
AB  - Determination of a protein structure requires a series of decisions and 
      processes, starting with target selection, through cloning, expression, 
      purification, and finally structure determination. Structural genomics projects 
      may distribute these steps among several different groups of researchers. 
      Although this division may achieve a lower cost per solved structure, it creates 
      a unique set of challenges for integrating and passing information on the 
      progress of a given target across several functional divisions. Laboratory 
      information management systems (LIMS) are essential for gathering this 
      information, but may not display the progress of a given target in an intuitive 
      way. In addition, structural genomics projects funded by the Protein Structure 
      Initiative (PSI) are obliged to disseminate data regularly to the TargetDB and 
      PepcDB data repositories, and this requires the creation of specialized views of 
      the data. We report here how the flow of a target through a structural genomics 
      pipeline and reports to TargetDB and PepcDB can be abstracted as directed acyclic 
      graphs or trees. To implement this kind of display, we created software that 
      tracks the flow of activity leading toward protein structure determination and 
      prepares XML reports as input to TargetDB and PepcDB. The target tracing software 
      consists of a set of Perl CGI scripts that integrate with the Graphviz 
      visualization system to provide a graphical, user-friendly Web interface. The 
      database reporting software, also coded in Perl, transfers large-scale genomics 
      data from our LIMS into a PepcDB reportable XML file. This software package has 
      facilitated inter-group communication, improved the quality and accuracy of 
      information in our LIMS, and increased the efficiency and accuracy of our reports 
      to PepcDB.
FAU - Pan, Xiaokang
AU  - Pan X
AD  - Center for Eukaryotic Structural Genomics, Department of Biochemistry, University 
      of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
FAU - Wesenberg, Gary E
AU  - Wesenberg GE
FAU - Markley, John L
AU  - Markley JL
FAU - Fox, Brian G
AU  - Fox BG
FAU - Phillips, George N Jr
AU  - Phillips GN Jr
FAU - Bingman, Craig A
AU  - Bingman CA
LA  - eng
GR  - U54 GM07901/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20080131
PL  - Netherlands
TA  - J Struct Funct Genomics
JT  - Journal of structural and functional genomics
JID - 101128185
RN  - 0 (Proteins)
SB  - IM
MH  - *Database Management Systems
MH  - *Databases, Protein
MH  - *Genomics
MH  - Information Storage and Retrieval/*methods
MH  - Proteins/*chemistry/*metabolism
MH  - Software
EDAT- 2008/02/01 09:00
MHDA- 2008/06/06 09:00
CRDT- 2008/02/01 09:00
PHST- 2007/08/01 00:00 [received]
PHST- 2007/11/13 00:00 [accepted]
PHST- 2008/02/01 09:00 [pubmed]
PHST- 2008/06/06 09:00 [medline]
PHST- 2008/02/01 09:00 [entrez]
AID - 10.1007/s10969-007-9037-0 [doi]
PST - ppublish
SO  - J Struct Funct Genomics. 2007 Dec;8(4):209-16. doi: 10.1007/s10969-007-9037-0. 
      Epub 2008 Jan 31.