Difference between revisions of "Systems curation"
m (→System) |
m |
||
| Line 18: | Line 18: | ||
== Biocuration == | == Biocuration == | ||
| + | Curation<ref>The etymology of ''curator'' ultimately derives from latin ''curator'' (guardian, agent), a derivation of ''curare'' (to care for, to cure).</ref> is not the same as our normal, day to day reading and the kind of report writing you may be used to. Curation does not only '''collect and present''' facts, but ensures the facts are '''valid''', '''complete''' and '''verifiable'''. | ||
| + | |||
| + | To '''collect and present''' your facts you: | ||
| + | * plan explicitly what information items you need to collect (and record your plan); | ||
| + | * define how your information will be structured; | ||
| + | * commit your information to an appropriate resource: a structured document, a spreadsheet, or a database, where it can be found and retrieved. | ||
| + | |||
| + | To ensure your information is '''valid''' you: | ||
| + | * define your terms in an ontology (preferred), or controlled vocabulary to ensure that all terms across a curation project are used consistently, with identical semantics; | ||
| + | * work from reliable sources; | ||
| + | * carefully assess facts for consistency (and record conflicts). | ||
| + | |||
| + | To ensure your results are '''complete''', you | ||
| + | * employ multiple, current information sources; | ||
| + | * explicitly express your expectations about complete information so you recognize when information is missing (i.e. you work with [https://github.com/hyginn/SyRO '''SyRO''']); | ||
| + | * record open questions. | ||
| + | |||
| + | To ensure your results are '''verifiable''', you | ||
| + | * record the process: where did you find the information, why did you use that resource; | ||
| + | * record the evidence and what is the evidence that the information is reliable. | ||
{{Vspace}} | {{Vspace}} | ||
| Line 37: | Line 57: | ||
== Process == | == Process == | ||
| + | |||
| + | |||
| + | |||
| + | *What are the "components" – Genes? Proteins? Metabolites? Environmental conditions? | ||
| + | *What exactly do we mean by "collaborating" – what makes a relationship a collaboration? And what is its goal? | ||
| + | *What do we mean by "emergent"? Is the mention of collaborating and emergent redundant? | ||
| + | *What do we mean by "behaviour"? | ||
{{Vspace}} | {{Vspace}} | ||
== Resources == | == Resources == | ||
| − | + | {{Smallvspace}} | |
| − | + | * [[BIN-SYS-Concepts|the ABC '''Systems Concepts''' unit]] | |
Revision as of 12:10, 23 February 2019
Systems curation
Notes on curating a biological system.
Biocuration
Curation[1] is not the same as our normal, day to day reading and the kind of report writing you may be used to. Curation does not only collect and present facts, but ensures the facts are valid, complete and verifiable.
To collect and present your facts you:
- plan explicitly what information items you need to collect (and record your plan);
- define how your information will be structured;
- commit your information to an appropriate resource: a structured document, a spreadsheet, or a database, where it can be found and retrieved.
To ensure your information is valid you:
- define your terms in an ontology (preferred), or controlled vocabulary to ensure that all terms across a curation project are used consistently, with identical semantics;
- work from reliable sources;
- carefully assess facts for consistency (and record conflicts).
To ensure your results are complete, you
- employ multiple, current information sources;
- explicitly express your expectations about complete information so you recognize when information is missing (i.e. you work with SyRO);
- record open questions.
To ensure your results are verifiable, you
- record the process: where did you find the information, why did you use that resource;
- record the evidence and what is the evidence that the information is reliable.
System
A system maps a set of collaborating components to its emergent behaviour.
This operational definition applies when we consider instances of systems in a "bottom up" approach (synthetic – how is the system built from its components) as well as a "top down" approach (analytic – how can the behaviour of the system be explained from its constituents). It emphasizes observables (behaviour), clarifies the conceptual nature of system (it maps), it has a scope and boundaries (a set), it is decomposable (components), it has a structure (induced by collaborations), its components are necessary and sufficient (leading to emergent behaviour).
System curation goals
Process
- What are the "components" – Genes? Proteins? Metabolites? Environmental conditions?
- What exactly do we mean by "collaborating" – what makes a relationship a collaboration? And what is its goal?
- What do we mean by "emergent"? Is the mention of collaborating and emergent redundant?
- What do we mean by "behaviour"?
Resources
Notes
- ↑ The etymology of curator ultimately derives from latin curator (guardian, agent), a derivation of curare (to care for, to cure).
