Discussion on Proposed Change to Pathway Definition

Return to BRIDG

CLOSED - Proposed Change to Pathway Definition (row 54)

Original Definition

DEFINITION: A set or series of interactions and processes, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical, or other reasons.

Comment Requested: In interest of re-using existing standards, should the above definition of Pathway be replaced by the following from the NLM - A series of actions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move. [Source: http://www.genome.gov/27530687]

EXAMPLE(S): Notch signaling pathway

OTHER NAME(S):

NOTE(S):

Ballot Comment

An interaction is a process. A series is a set. It does not matter who has found it useful to the definition. Part of a pathway can take place outside cells, for example, interactions with the extracellular matrix.

Proposed Definition

DEFINITION: A set of related molecular biological processes that leads to a biological change or event.

EXAMPLE(S): Notch signaling pathway

OTHER NAME(S):

NOTE(S):

Proposed Disposition

Persuasive

Proposed Disposition Comment

Sounds like this might be a clarification helping to make the definition and example simpler. Need to verify the proposed change is OK with the life sciences subject matter experts who originally helped develop the LSDAM semantics to ensure their use case is correctly represented.

Initial Discussion

Review proposed change with LSDAM SMEs to ensure change is consistent with their original use case for the concept. Also see disposition comments and recommendation on Gene item a few rows above.

Outstanding Questions

• Life Science SMEs: Is the proposed changes consistent with the original use case for your concept?
• Anyone: Can someone provide a comprehensive, realistic and meaningful set of example values that uses the same overall scenario across all classes in the Molecular Biology sub-domain?

Responses

Lauren Becnel: Please use the NLM definition and examples (A series of actions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move.) from the previous commenter. Biological processes are NOT just molecular or cellular, whereas pathways are.

Q from WENDY (TYPE: DEFN): There appears to be a potential conflict between Mollie's comment that "Part of a pathway can take place outside cells, for example, interactions with the extracellular matrix." and the NLM definition that says " A series of actions among molecules in a cell that..." - Is the apparent conflict real?

DISCUSSION 20160225: Lauren will review the NLM definition and see if there could be an adaptation of it that would satisfy Mollie’s concern: A series of actions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move. [Source: http://www.genome.gov/27530687]

Lauren Becnel, 20160226: 'A series of actions among molecules in or associated with a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move. [Adapted from: http://www.genome.gov/27530687]'

Return to BRIDG