PICA Draft Example Part Declarations


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Ralph Santos PICA Draft Proposal: Example Part Declarations 2008-03-06

Introduction
Here are some example declarations. These examples are intended to illustrate how the draft proposal would be applied to specific parts, and to illustrate both how annotations are formed and the expressive range of the language. They are given in a simple S-expression syntax which is intended to be as close to technologically neutral as possible. The examples are not intended to be authoritative descriptions of the given parts and may be subject to change as the standard evolves. Also, the S-expression syntax is used primarily for illustrative purposes within the specification documents and is not necessarily intended to be use by any particular annotator or processed by any particular application.

Part Declarations
BBa_F2620 is a simple example part, a promoter actuated by 3OC6HSL.

(pica-part-declaration (version 'draft) (partname 'BBa_F2620)  (composition (SO:forward   (SO:promoter_region y)    (SO:CDS y)    (SO:terminator Y)    (trans-upstream-start N)    (trans-downstream-end Y)   ) ; // nothing on the reverse strand [?]- add negative assertions? ) (terminals pubchem:sid:24896225 CDS ) (interactions (reg-relations   ((pubchem:sid:24896225 preceded_by CDS) SO:transcriptionally_induced)   ) (events nil) ) )

BBa_I744104 illustrates a more complicated part declaration. This part has inside of it an operon for expressing a Tet repressor that suppresses transcription of the Enhanced YFP protein.

(pica-part-declaration (version 'draft) (part-name 'BBa_I744104)  (composition (SO:forward   (SO:promoter_region y)    (SO:CDS y)    (SO:terminator Y)    (trans-upstream-start N)    (trans-downstream-end N)   ) ; // nothing on the reverse strand [?]- add negative assertions? ) (terminals pubchem:cid:5497101 '?tetR '?EYFP)  (interactions (reg-relations   (('?tetR '?EYFP) SO:transcriptionally_repressed)    ((pubchem:cid:5497101 '?EYFP) SO:transcriptionally_promoted)   ) (events nil) ) )

BBa_J01002 is a part which contains a transcription origin site for cell conjugation, also known as horizontal transfer. While not the most frequently cited part type, since the Sequence Ontology has a term for the transcription origin it can be expressed as easily as any other part.

(pica-part-declaration (version 'draft) (part-name 'BBa_J01002)  (composition (SO:forward   (SO:promoter_region N)    (SO:CDS N)    (SO:terminator N)    (SO:oriT Y)    (trans-upstream-start N)    (trans-downstream-end N)   ) ; // nothing on the reverse strand [?]- add negative assertions? ) (interactions (reg-relations nil) (events nil) ) )

Bba_J45200 is the banana generator part. This illustrates how part activities not directly tied to gene regulation can be expressed in the language. It also illustrates how constitutive expression can be declared within the framework.

(pica-part-declaration (version 'draft) (part-name 'BBa_J45200)  (composition (SO:forward   (SO:promoter_region y)    (SO:CDS y)    (SO:terminator Y)    (trans-upstream-start N)    (trans-downstream-end N)   ) ; // nothing on the reverse strand [?]- add negative assertions? ) (terminals pubchem:cid:31260 pubchem:cid:31276 '?ATF1)  (interactions (reg-relations   (('?ATF1) SO:transcriptionally_constitutive)   ) (events   ((pubchem:cid:31260 pubchem:cid:31276) SBO:participant ('?ATF1 SBO:catalyst))  ) ) )

BBa_R0051 ; demo: reverse strand feature declaration ; R0051 is forward version of I742126 ; (pica-part-declaration (version 'draft) (part-name 'BBa_R0051)  (composition (SO:forward   (SO:promoter_region y)    (SO:CDS N)    (SO:terminator N)    (trans-upstream-start N)    (trans-downstream-end Y)   ) ; // nothing on the reverse strand [?]- add negative assertions? ) (terminals pubchem:'?Lambda-cI SO:CDS)  (interactions (reg-relations   (('?Lambda-cI SO:CDS) SO:transcriptionally_induced)   ) (events nil) ) )

BBa_I742126 is the reverse of R0051. This demonstrates what reverse strand declarations would look like.

(pica-part-declaration (version 'draft) (part-name 'BBa_I742126)  (composition (SO:forward   (SO:promoter_region N)    (SO:CDS N)    (SO:terminator N)    (trans-upstream-start N)    (trans-downstream-end N)   ) (SO:reverse   (SO:promoter_region y)    (SO:CDS N)    (SO:terminator N)    (trans-upstream-start N)    (trans-downstream-end Y)   ) ; // nothing on the reverse strand [?]- add negative assertions? ) (terminals pubchem:'?Lambda-cI SO:CDS)  (interactions (reg-relations   (('?Lambda-cI SO:CDS) SO:transcriptionally_induced)   ) (events nil) ) )

Bba_G00100 is an unusual part in that it doesn't encode any parts for gene regulation, but rather simply contains a priming site for use with a plasmid designed for Biobrick work, PsB1AT3. However, since the Sequence Ontology has terms to describe priming sites, it can be expressed as a part declaration easily.

(pica-part-declaration (version 'draft) (part-name 'BBa_G00100)  (composition (SO:forward   (SO:promoter_region N)    (SO:CDS N)    (SO:terminator N)    (trans-upstream-start N)    (trans-downstream-end N)    (SO:primer_binding_site Y)   ) (terminals nil) (interactions  (reg-relations nil)   (events nil)  ) )

PsB1AT3 isn't a part in the strictest sense of the word, but rather a plasmid used for part construction. However, here it is written up as a part declaration to illustrate the expressive range that the Sequence Ontology gives to the language.

(pica-part-declaration (version 'draft) (part-name 'PsB1AT3)  (composition (SO:forward   (SO:promoter_region Y)    (SO:CDS Y)    (SO:terminator Y)    (trans-upstream-start N)    (trans-downstream-end N)    (SO:primer_binding_site Y)    (SO:origin_of_replication y)   ) (terminals '?AmpR '?TetR) (interactions  (reg-relations ((?'TetR) SO:transcriptionally_constitutive) ((?'AmpR) SO:transcriptionally_constitutive) )  (events nil)  ) )

Notes on Chemical Citations
Here's the references I used as the basis for the chemical citations. I don't have any pretense of being authoritative on biochemistry or compound databases. This information is included to make it easier to clean up any errors on my part.


 * 3-oc6-hsl

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=24896225 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=688505


 * tetracycline

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5497101


 * isoamyl alcohol

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=31260


 * isoamyl acetate

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=31276


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