Difference between revisions of "User:Scmohr/Gray box"

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Comments are given in <SPAN style= 'color:red'>''red italics.''</span>.  Words to appear in the "gray box" are in <SPAN style= 'color:blue'>'''bold blue.'''</span> Simple explanatory notes are in plain black text. The intent is for each item in the gray box to have a descriptive, clickable link.
 
Comments are given in <SPAN style= 'color:red'>''red italics.''</span>.  Words to appear in the "gray box" are in <SPAN style= 'color:blue'>'''bold blue.'''</span> Simple explanatory notes are in plain black text. The intent is for each item in the gray box to have a descriptive, clickable link.
 +
 +
'''DISCLAIMER'''
 +
 +
'''Note:''' The database links in this box refer to reference information that '''may not ''exactly'' correspond to a given part''', since by definition the parts have been engineered.
 +
 +
<SPAN style= 'color:red'>''This statement needs to appear in every box, perhaps on the side or at the bottom.''</span>
  
 
===Box Heading:===
 
===Box Heading:===
  
−
<SPAN style= 'color:blue'>'''REFERENCE INFORMATION LINKS FOR ___________'''</span> (part number inserted automatically)
+
<SPAN style= 'color:blue'>'''INFORMATION LINKS FOR ___________'''</span> (part number inserted automatically)
  
 
===Box Content===
 
===Box Content===
  
−
<SPAN style= 'color:blue'>'''Source of DNA sequence:'''</span>
+
<SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span>
  
−
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> <SPAN style= 'color:red'>''There are two different kinds of GenBank numbers, GI numbers and Accession/Version numbers.  It will be important to have that clarified. (Maybe it doesn't matter as long as they are clickable links...) The GI numbers are less ambiguous.''</span>
+
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> <SPAN style= 'color:red'>''There are two different kinds of GenBank numbers, "GI" numbers and "Accession/Version" numbers.  It will be important to have that clarified in the part-deposit instructions. (Maybe it doesn't matter as long as they are clickable links...) The GI numbers are less ambiguous.''</span>
 
*<SPAN style= 'color:blue'>'''Other: ___________'''</span> <SPAN style= 'color:red'>''Possible "other" links include other databases (for example, RNA databases) or a laboratory webpage.''</span>
 
*<SPAN style= 'color:blue'>'''Other: ___________'''</span> <SPAN style= 'color:red'>''Possible "other" links include other databases (for example, RNA databases) or a laboratory webpage.''</span>
  
 
<SPAN style= 'color:blue'>'''Structure (PDB_ID): ___________''' </span>
 
<SPAN style= 'color:blue'>'''Structure (PDB_ID): ___________''' </span>
  
−
<SPAN style= 'color:blue'>'''UniProt (Accession No.): ___________''' </span>
+
<SPAN style= 'color:blue'>'''UniProt (Accession no.): ___________''' </span> <SPAN style= 'color:red'>''Like GenBank, UniProt also uses two different kinds of identifier, "Accession number" and "Entry name."  Only Accession numbers work as links.  When users search UniProt, however, the hit lists come back with entry names displayed and a naive user might try to put that in as a link.  A specific instruction (such as: For links to UniProt, ''always'' use the "Accession number," ''not'' the "Entry name") should be provided''</span>
  
−
<SPAN style= 'color:blue'>'''Biological Origin: ___________'''</span><SPAN style= 'color:red'>''The link can go to NCBI Taxonomy page -- see, for example, http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy.''</span>
+
<SPAN style= 'color:blue'>'''Biological origin: ___________'''</span><SPAN style= 'color:red'>''The link can go to one of the NCBI Taxonomy pages -- see, for example, http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy.''</span>
  
−
<SPAN style= 'color:blue'>Key references: ___________ </span>(Up to three PubMed IDs)
+
<SPAN style= 'color:blue'>'''Literature references: ___________''' </span>(Up to three PubMed IDs)
  
 
<SPAN style= 'color:blue'>'''Designer homepage: ___________'''</span><SPAN style= 'color:red'>''This link could be to an individual, an iGEM team or a laboratory.''</span>
 
<SPAN style= 'color:blue'>'''Designer homepage: ___________'''</span><SPAN style= 'color:red'>''This link could be to an individual, an iGEM team or a laboratory.''</span>
  
−
=='''For Protein Coding Sequences -- Enzymes:'''==
+
=='''For Protein Coding Sequences - Enzymes:'''==
  
 
===Box Heading:===
 
===Box Heading:===
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===Box Content===
 
===Box Content===
  
−
<SPAN style= 'color:blue'>'''Source of DNA sequence:'''</span>
+
<SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span>
  
 
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span>  
 
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span>  
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<SPAN style= 'color:blue'>'''Biological Origin: ___________'''
 
<SPAN style= 'color:blue'>'''Biological Origin: ___________'''
  
−
<SPAN style= 'color:blue'>'''Key references: ___________ (Up to three PubMed IDs)
+
<SPAN style= 'color:blue'>'''Literature references: ___________''' </span> (Up to three PubMed IDs)
 +
 
 +
<SPAN style= 'color:blue'>'''Designer homepage: ___________'''
 +
 
 +
=='''For Protein Coding Sequences - Enzyme Example:'''==
 +
 
 +
===<SPAN style= 'color:brown'>Box Heading:</span>===
 +
 
 +
'''INFORMATION LINKS FOR <SPAN style= 'color:blue'>[https://parts.igem.org/Part:BBa_J45014 BBa_J45014]'''</span>
 +
 
 +
===<SPAN style= 'color:brown'>Box Content:</span>===
 +
 
 +
'''NAME: <SPAN style= 'color:blue'> [http://www.expasy.org/enzyme/2.3.1.84 Alcohol O-acetyltransferase 1]''' </span>
 +
 
 +
'''Nickname: AAT 1 ''[[or]] ATF1'''''
 +
 
 +
'''Source of ''original'' DNA sequence:'''<SPAN style= 'color:blue'>  </span>
 +
 
 +
*'''GenBank <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=1420813 GI: 1420813'''] </span>
 +
*'''Other: n/a'''
 +
 
 +
'''Structure (PDB_ID): n/a''' </span>
 +
 
 +
'''UniProt (Accession No.): <SPAN style= 'color:blue'>[http://www.uniprot.org/uniprot/P40353 P40353]''' </span>
 +
 
 +
'''Reaction (EC No.): <SPAN style= 'color:blue'>[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/84.html EC 2.3.1.84]''' </span>
 +
 
 +
'''Biological Origin: <SPAN style= 'color:blue'> [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932&lvl=3&lin=f&keep=1&srchmode=1&unlock ''Saccharomyces cerevisiae]'''''</span>
 +
 
 +
'''Literature references (PubMed IDs):
 +
<SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/pubmed/8085822?dopt=Abstract '''PM 8085822,'''] [http://www.ncbi.nlm.nih.gov/pubmed/12937998?dopt=Abstract '''PM 12937998,'''] [http://www.ncbi.nlm.nih.gov/pubmed/17891501?dopt=Abstract '''PM 17891501''']</span>
 +
 
 +
'''Designer: <SPAN style= 'color:blue'>[http://parts2.mit.edu/wiki/index.php/MIT_2006 Andre Green''']</span>
 +
 
 +
=='''For Protein Coding Sequences - Repressors and Activators:'''==
 +
 
 +
===Box Heading:===
 +
 
 +
<SPAN style= 'color:blue'>'''REFERENCE INFORMATION LINKS FOR ___________'''</span> (part number inserted automatically)
 +
 
 +
===Box Content===
 +
 
 +
<SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span>
 +
 
 +
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span>
 +
*<SPAN style= 'color:blue'>'''Other: ___________'''
 +
 
 +
<SPAN style= 'color:blue'>'''Structure (PDB_ID): ___________''' </span>
 +
 
 +
<SPAN style= 'color:blue'>'''UniProt (Accession No.): ___________''' </span>
 +
 
 +
<SPAN style= 'color:blue'>'''Biological Origin: ___________'''
 +
 
 +
<SPAN style= 'color:blue'>'''Literature references: ___________''' </span> (Up to three PubMed IDs)
 +
 
 +
<SPAN style= 'color:blue'>'''Designer homepage: ___________'''
 +
 
 +
=='''For Protein Coding Sequences - Repressors and Activators - Example:'''==
 +
 
 +
===<SPAN style= 'color:brown'>Box Heading:</span>===
 +
 
 +
'''INFORMATION LINKS FOR <SPAN style= 'color:blue'>[https://parts.igem.org/Part:BBa_C0040 BBa_C0040]'''</span>
 +
 
 +
===<SPAN style= 'color:brown'>Box Content:</span>===
 +
 
 +
'''NAME: <SPAN style= 'color:blue'>Tetracycline repressor from transposon Tn10'''</span>]
 +
 
 +
'''Nickname: tetR '''
 +
 
 +
'''Source of ''original'' DNA sequence:'''<SPAN style= 'color:blue'>  </span>
 +
 
 +
*'''GenBank <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=42494906 GI: 42494906'''] </span>
 +
'''Other: n/a'''
 +
 
 +
'''Structure (PDB_ID): [http://www.pdb.org/pdb/cgi/explore.cgi?pdbId=2NS7 2NS7]''' </span>
 +
 
 +
'''UniProt (Accession No.): <SPAN style= 'color:blue'>[http://www.uniprot.org/uniprot/Q6QR72 Q6QR72]''' </span>
 +
 
 +
'''Biological Origin: <SPAN style= 'color:blue'> [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562 Escherichia coli'''] </span>
 +
 
 +
'''Literature references (PubMed IDs):
 +
<SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/pubmed/9092630?dopt=Abstract '''PM 9092630'''] </span>
 +
 
 +
'''Designer: <SPAN style= 'color:blue'> June Rhee, Connie Tao, Ty Thomson, Louis Waldman'''</span>
 +
 
 +
=='''For Terminators:'''==
 +
 
 +
===Box Heading:===
 +
 
 +
<SPAN style= 'color:blue'>'''REFERENCE INFORMATION LINKS FOR ___________'''</span> (part number inserted automatically)
 +
 
 +
===Box Content===
 +
 
 +
<SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span>
 +
 
 +
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span>
 +
*<SPAN style= 'color:blue'>'''Other: ___________'''
 +
 
 +
<SPAN style= 'color:blue'>'''3D-Structure (NDB_ID): ___________''' </span>
 +
 
 +
<SPAN style= 'color:blue'>'''Rfam entry: ___________'''
 +
 
 +
<SPAN style= 'color:blue'>'''Secondary-Structure Prediction Tools: ___________'''
 +
 +
<SPAN style= 'color:blue'>'''Biological Origin: ___________'''
 +
 
 +
<SPAN style= 'color:blue'>'''Literature references: ___________''' </span> (Up to three PubMed IDs)
  
 
<SPAN style= 'color:blue'>'''Designer homepage: ___________'''
 
<SPAN style= 'color:blue'>'''Designer homepage: ___________'''

Latest revision as of 21:25, 17 July 2008

This page will contain drafts of potential "Gray Boxes" for different categories of basic parts.

For all basic parts:

Comments are given in red italics.. Words to appear in the "gray box" are in bold blue. Simple explanatory notes are in plain black text. The intent is for each item in the gray box to have a descriptive, clickable link.

DISCLAIMER

Note: The database links in this box refer to reference information that may not exactly correspond to a given part, since by definition the parts have been engineered.

This statement needs to appear in every box, perhaps on the side or at the bottom.

Box Heading:

INFORMATION LINKS FOR ___________ (part number inserted automatically)

Box Content

Source of original DNA sequence:

  • GenBank GI: ___________ There are two different kinds of GenBank numbers, "GI" numbers and "Accession/Version" numbers. It will be important to have that clarified in the part-deposit instructions. (Maybe it doesn't matter as long as they are clickable links...) The GI numbers are less ambiguous.
  • Other: ___________ Possible "other" links include other databases (for example, RNA databases) or a laboratory webpage.

Structure (PDB_ID): ___________

UniProt (Accession no.): ___________ Like GenBank, UniProt also uses two different kinds of identifier, "Accession number" and "Entry name." Only Accession numbers work as links. When users search UniProt, however, the hit lists come back with entry names displayed and a naive user might try to put that in as a link. A specific instruction (such as: For links to UniProt, always use the "Accession number," not the "Entry name") should be provided

Biological origin: ___________The link can go to one of the NCBI Taxonomy pages -- see, for example, http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy.

Literature references: ___________ (Up to three PubMed IDs)

Designer homepage: ___________This link could be to an individual, an iGEM team or a laboratory.

For Protein Coding Sequences - Enzymes:

Box Heading:

REFERENCE INFORMATION LINKS FOR ___________ (part number inserted automatically)

Box Content

Source of original DNA sequence:

  • GenBank GI: ___________
  • Other: ___________

Structure (PDB_ID): ___________

UniProt (Accession No.): ___________

Reaction (EC No.): ___________

Biological Origin: ___________

Literature references: ___________ (Up to three PubMed IDs)

Designer homepage: ___________

For Protein Coding Sequences - Enzyme Example:

Box Heading:

INFORMATION LINKS FOR BBa_J45014

Box Content:

NAME: [http://www.expasy.org/enzyme/2.3.1.84 Alcohol O-acetyltransferase 1]

Nickname: AAT 1 or ATF1

Source of original DNA sequence:

  • GenBank [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=1420813 GI: 1420813]
  • Other: n/a

Structure (PDB_ID): n/a

UniProt (Accession No.): [http://www.uniprot.org/uniprot/P40353 P40353]

Reaction (EC No.): [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/84.html EC 2.3.1.84]

Biological Origin: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932&lvl=3&lin=f&keep=1&srchmode=1&unlock Saccharomyces cerevisiae]

Literature references (PubMed IDs): [http://www.ncbi.nlm.nih.gov/pubmed/8085822?dopt=Abstract PM 8085822,] [http://www.ncbi.nlm.nih.gov/pubmed/12937998?dopt=Abstract PM 12937998,] [http://www.ncbi.nlm.nih.gov/pubmed/17891501?dopt=Abstract PM 17891501]

Designer: [http://parts2.mit.edu/wiki/index.php/MIT_2006 Andre Green]

For Protein Coding Sequences - Repressors and Activators:

Box Heading:

REFERENCE INFORMATION LINKS FOR ___________ (part number inserted automatically)

Box Content

Source of original DNA sequence:

  • GenBank GI: ___________
  • Other: ___________

Structure (PDB_ID): ___________

UniProt (Accession No.): ___________

Biological Origin: ___________

Literature references: ___________ (Up to three PubMed IDs)

Designer homepage: ___________

For Protein Coding Sequences - Repressors and Activators - Example:

Box Heading:

INFORMATION LINKS FOR BBa_C0040

Box Content:

NAME: Tetracycline repressor from transposon Tn10]

Nickname: tetR

Source of original DNA sequence:

  • GenBank [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=42494906 GI: 42494906]

Other: n/a

Structure (PDB_ID): [http://www.pdb.org/pdb/cgi/explore.cgi?pdbId=2NS7 2NS7]

UniProt (Accession No.): [http://www.uniprot.org/uniprot/Q6QR72 Q6QR72]

Biological Origin: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562 Escherichia coli]

Literature references (PubMed IDs): [http://www.ncbi.nlm.nih.gov/pubmed/9092630?dopt=Abstract PM 9092630]

Designer: June Rhee, Connie Tao, Ty Thomson, Louis Waldman

For Terminators:

Box Heading:

REFERENCE INFORMATION LINKS FOR ___________ (part number inserted automatically)

Box Content

Source of original DNA sequence:

  • GenBank GI: ___________
  • Other: ___________

3D-Structure (NDB_ID): ___________

Rfam entry: ___________

Secondary-Structure Prediction Tools: ___________

Biological Origin: ___________

Literature references: ___________ (Up to three PubMed IDs)

Designer homepage: ___________