TRANSPATH Professional Documentation

PATHWAY

Pathway

The pathway flat file contains two types of entities: pathways and chains. Pathways reflect canonical pathways for specific signaling molecules (mostly ligands or receptors) and are made up of one or more chains. Chains are sets of consequent reactions, i.e. the reactions contain common molecules. Chains that are linked to pathways consist of reactions of the type 'pathway step' and in some cases 'indirect'. Chains can have bifurcations and even loops (if they carry a regulatory meaning). Figure 1 shows how pathways and chains are connected to the reaction hierarchy.

pathway and reaction hierarchy
Fig.1: Relationship of reaction hierarchy and pathway/chains. Chains and on the top-level pathways group pathway step reactions, whereas pathway step reactions as central element of the reaction hierarchy group molecular evidence reactions.

The construction of chains and pathways is based on recent (primary and review) literature and on the expert knowledge of the annotator who has worked intensely on the specific topic. In some cases, when a sequence of reactions has been reported by one primary paper, the chain is labelled in the type field as 'evidence chain'. We assume that the physiological relevance of a reaction sequence is higher when one group has proved it in a consistent experimental system.

A visualization of the pathways is accessible as prepared PathwayBuilder™ maps. The maps can be expanded at points of interest and can be modified the same as normal PathwayBuilder™ outputs. These pathway representations have their counterparts in the hand-drawn clickable maps, which contain more condensed information but are static.

Fields

It should be noted that in individual entries, some fields might be empty. In this case, these fields are not displayed.

Field		Content and format
AC	Accession number	The accession number is the unique identifier for each entry. Its format is "CH" in capital letters followed by nine digits (e.g. CH000012345). If two entries have to be merged, the AC of the primary name is retained. The other AC will be stored in the secondary accession numbers (AS) field.
AS	Accession numbers, secondary	The secondary accession numbers are optional alternate identifiers for each entry. They are of the form defined in AC, separated by semicolons, and are created when two entries are merged.
DT	Created by	The name of the curator who created the entry. E-mail your feedback directly to the curator.
DT	Updated by	The name of the curator who last updated the entry. E-mail your feedback directly to the curator.
CO	Copyright Information
TY	Type	Marks the kind of chain the entry tells about. Terms used: pathway chain evidence chain
NA	Name	Names of pathway entries are oriented on characteristic molecules (e.g. ligands, receptors, transcription factors) and are the same as for the respective prepared PathwayBuilder™ maps and the hand-drawn maps. Names of chain entries address start and end molecules (A ---> X), which in case of bifurcations can be several (A, B ---> X, Y, Z). To differentiate between chains with the same start and end molecules, a prominent molecule of the in-between path is indicated (A ---M---> X). In some cases the name is a term for a physiological process such as G1 phase (cell cycle).
HP	Pathway level	Lists all pathways that are superordinated.
HC	Chain level	Lists all chains that are subordinated.
CC	Comments	A list of annotates. Further information about the different categories of comments is available under Annotate.
XN	Reactions involved	A list of all reactions the pathway/chain consists of.
MO	Molecules involved	A list of all molecules the pathway/chain consists of.
RN	Reference number	[consecutive entry reference number]. A list of the papers from which the information in this entry was extracted. For further information please see Reference.
RX	Medline database hyperlink	The PMID number in PubMed
RA	Reference author(s)	list of authors Reference
RT	Reference title	Reference
RL	Reference publication	Reference