Shorthand
Overview
The two kinds of experiments:
(1) Experiments that describe the state of something in the cell under defined conditions. A datum derived from these experiments is called a SDatum (for state datum).
(2) Experiments that describe the change in the state of something in the cell when the defined conditions are altered. A datum derived from this kind of experiment is called a CDatum (for change datum).
The structure of a datum
The first line of a datum
A "basic" experiment:
A system is defined in regards to a testable parameter (SDatum)
The system is perturbed and the effect on the testable parameter is determined. (CDatum)
An experiment with "extras":
A change is made to the basic experiment and the change in the effect of the testable parameter is determined.
The first line of the datum supplies information about the basic experiment.
Format for CDatums:  Subject Assay Change Treatment (times)
Format for SDatums:  Subject Assay Detectablility
The cells line describes the cells and the medium/conditions used in the basic experiment.  Any attributes such as expressed or knocked-out proteins not mentioned on the first line are listed here.
The times line supplies additional information about the times studied and the relative change (if any) in the reponse.
The oligo line supplies information about the oligonucleotide used in an oligo-binding assay.
The IPfrom line supplies information about the source of an immunoprecipitate used in a test-tube experiment.  If more than one immunoprecipitate are used in an experiment they are numbered (e.g  IP1from and IP2from).
The extras describe changes made to the basic experiment and the influence the changes have on the results.
The source line supplies the PubMed ID of the reference and the figure or table that displays the data.
The comments line provides information not mentioned in the other lines.
First Line:  Subject Assay Change Stimulus
Subject: Subjects can be Proteins, Genes, or Chemicals
When the subject is a Protein:
prefixProtein(mutation){modification}[Handle]IP
prefix: tells whether a protein is endogenous or exogenous
if the Protein has no prefix, then it is an endogenous protein
if prefixed with "x" then it is a protein expressed ectopically in a eukaryotic cell
if prefixed with "k" then it is a mutated protein expressed from a "knockin" sequence driven by the endogenous promoter.
if prefixed with "r" then it is a protein expressed in a prokaryotic cell and purified
if prefixed with "p" then it is a protein that has been purified from mammalian tissues
Protein can be BProtein, Family, or Composite
Only BProteins can have mutations
mutation: a change in the sequence of a protein (optional)
modification: a chemical modification of a protein after its translation (optional)
Handle: tells how the subject is identified (required for everything except rProteins)
IP: used if the subject is an immunoprecipitate
When the subject is a gene:
BProtein-gene
In Pathway Logic genes use the Protein name followed by -gene.  Genes do not have prefixes, mutations, or modifications.  They do not require handles because they are easily identified by their sequences.
When the subject is a chemical:
Chemical[Handle]
Handle: tells how the subject is identified (required)
Assay:  Possible Assays with syntax are listed in the Assays section
Change: Possible changes are
is increased
is decreased
is unchanged
is repressed
is detectable
is undetectable
Stimulus:
Stimulus is omitted if 'is detectable' or 'is undetectable' is used.
Use:  irt Treatment (times)
when a cell is stimulated by the addition of something (Protein, Peptide, Chemical) to the supernatant or a change in its environment (adherence, UV light, mechanical stress).
If only one time point is measured, it is placed in parenthesis after the treatment
If more than one time point is measured, use (times).  This tells the reader that there is a time course with relative responses later in the datum (see Times line)
Use:  itpo xBProtein
when the effects of Protein expression are being studied.
Time points are not used here because the length of time it takes to get Protein expression is longer than the scope of a STM model.
Use:  by Treatment
for experiments performed in the absence of intact cells.
Time points are not used here because we are only interested in the time it takes to pass a signal within the cell.
The cells Line:
cells: CellName<attributes> in Medium "other-stuff"
CellName:
Cell Lines:
In order to make our shorthand parsible, we have choosen or altered cell line names to make them unambiguous and machine readable.
Cell line names have the following characteristics:
Each name must be unique.
Names are representations or abbreviations of the most commonly used names.
Names only contain Latin letters and Arabic numerals.
Names do not contain spaces.
A list of the cell line names can be found in Cell Lines section.
The Cell Lines section also contains ATCC catalog numbers if available, synonyms, growth conditions, molecular charactistics, and references.  This information is by no means complete - but it has been used as a repository of information about the cell lines picked up during curation.
Primary Cells:
Primary Cells are given names based on the species and tissues from which they were derived and the purification methods used.
A list of the names used can be found in the Primary Cells section.
Tissues and other things:
In some experiments, the cells used can not be categorized as cell lines or primary cells.  In those case, the contents of the cells line is surrounded by quote marks.  This is a cue to the datum parser to treat the contents as a string.  It is a cue to the reader that the derivation of the cells is not described in this manual and that the reader has to hunt down the details from the original source.
examples:
attributes:
<Protein-null>  cell does not contain endogenous protein
<xProtein>  cells has been transfected (either stable or transiently) with a plasmid that expresses Protein.
<xProtein(mutation)>  cells has been transfected (either stable or transiently) with a plasmid that expresses Protein containing a mutation.
Medium:
BMHIS:  basal medium containing heat-inactivated serum
BMLS:  basal medium containing low serum
used when cells are "serum-starved"  or in less than 2% serum or "made quiescent"
BMS: basal medium containing serum
eg "growth medium"
note: BMS is used if no description of the medium is given
BSS: balanced salt solution
MNR: medium not reported
other-stuff:
any conditions that are common to all the samples in the experiment
The times Line:
This line shows the time points measured and the relative change in the response.
The response is shown by using "+" after each time point.  The number of "+"s used does not represent the size or intensity of the response, only the change in the size or intensity of the response.
Response times less than 1 min are not collected.
examples:
Extras:
Each extra line contains a refinement of the basic experiment that provides additional information about the influence of various parameters on the outcome.  These include:
The effect of the removal of a Protein or Proteins for a response to occur is is demonstrated by performing the basic the experiment using:
cells from knockout mice [KO]
cells known to be lacking the expression of the Protein [null-mut]
cells treated with RNAi or Antisense oligos [RNAi] [Antisense]
cells expressing a protein with dominant-negative mutations [addition]
cells expressing shRNAs against the protein [RNAi]
The effect of a protein feature or modification on the response is demonstrated by the expression of a protein either lacking the required feature or mutated to prevent the required modification.
The effect of chemical inhibitors and enhancers on the response is demonstrated by pretreating and/or cotreating the cells with the chemicals during the basic experiment.
The effect of other stimuli or stresses on the response is demonstrated by pretreating and/or cotreating the cells with the stimuli during the basic experiment.
reqs:
reqs: Protein [KO] | [RNAi] | [AntiSense] | [null-mut] | [DKO] | [DRNAi]
change or detectablity is significantly less or gone in the absence of an endogenous protein
reqs: xProtein [omission]
change or detectablity is significantly less or gone in the absence of an expressed protein
reqs: Chemical [omission]
change or detectablity is significantly less or gone in the absence of a chemical stimulus
does not req:
does not req: Protein [KO] | [RNAi] | [AS] | [null-mut]
change or detectablity is unchanged in the absence of an endogenous protein
does not req: xProtein [omission]
change or detectablity is unchanged in the absence of an expressed protein
does not req: Chemical [omission]
change or detectablity is unchanged in the absence of a chemical stimulus
enhanced by:
enhanced by: xProtein(mutation(s)) [addition]
a positive change or detectability is increased by the expression of a protein that is not expressed in the basic experiment
enhanced by: rProtein(mutation(s)) [addition]
a positive change or detectability is increased by the addition of a protein to the reaction described in the basic experiment
enhanced by: xProtein(mutation(s)) [substitution]
a positive change or detectability is increased by the substitution of a protein that is expressed in the basic experiment with a mutated variant
enhanced by: Chemical [addition] | [cotreatment] | [pretreatment]
a positive change or detectability is increased by addition of a chemical to the basic experiment
enhanced by: Stimulus (time(s)) [stim] | [cotreatment] | [pretreatment]
a positive change or detectability is increased by addition of a Ligand, anti-Receptor antibody, stress, or nutrient to the basic experiment
a chemical may be a stimulus if it produces a known response
inhibited by:
inhibited by: xProtein [addition]
a positive change or detectability is decreased by the expression of a protein that is not expressed in the basic experiment
inhibited by: rProtein [addition]
a positive change or detectability is decreased by the addition of a protein to the reaction described in the basic experiment
inhibited by: xProtein [substitution]
a positive change or detectability is decreased by the substitution of a protein that is expressed in the basic experiment with a mutated variant
inhibited by: rProtein [substitution]
a positive change or detectability is decreased by the substitution of a protein in the reaction described in the basic experiment with a mutated or modified variant
inhibited by: Chemical [addition] | [cotreatment] | [pretreatment]
a positive change or detectability is decreased by addition of a chemical to the basic experiment
inhibited by: Stimulus (time(s)) [stim] | [cotreatment] | [pretreatment]
a positive change or detectability is decreased by addition of a Ligand, anti-Receptor antibody, stress, or nutrient to the basic experiment
a chemical may be a stimulus if it produces a known response
repressed by:
repressed by: Protein [KO] | [RNAi] | [AntiSense] | [null-mut]
a positive change is significantly increased in the absence of an endogenous protein
reversed by:
reversed by: xProtein [substitution]
a positive or negative change is reversed by the substitution of a protein that is expressed in the basic experiment with a mutated variant
unaffected by:
unaffected by: xProtein [addition]
a positive change or detectability is unchanged by the expression of a protein that is not expressed in the basic experiment
unaffected by: rProtein [addition]
a positive change or detectability is unchanged by the addition of a protein to the reaction described in the basic experiment
unaffected by: xProtein [substitution]
a positive change or detectability is unchanged by the substitution of a protein that is expressed in the basic experiment with a mutated variant
unaffected by: Chemical [addition] | [cotreatment] | [pretreatment]
a positive change or detectability is unchanged by addition of a chemical to the basic experiment
unaffected by: Stimulus (time(s)) [stim] | [cotreatment] | [pretreatment]
a positive change or detectability is unchanged by addition of a Ligand, anti-Receptor antibody, stress, or nutrient to the basic experiment
a chemical may be a stimulus if it produces a known response
The source Line:
source: PMID-Fig-## or source: PMID-Table-##
source: PMID(D)