|
|
| 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 first line of a datum
|
|
|
|
| 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 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
|
|
|
|
| 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:
|
|
|
|
| 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:
|
|
|
|
| Handle: tells how the subject is identified (required)
|
|
|
|
| Assay: Possible Assays with syntax are listed in the Assays section
|
|
|
|
| Change: Possible changes are
|
|
|
|
| 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)
|
|
|
|
| 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.
|
|
|
|
| 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.
|
|
|
|
| cells: CellName<attributes> in Medium "other-stuff"
|
|
|
|
| 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 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.
|
|
|
|
| cells: "disaggregated embryonic day-12.5 mouse embryos"
|
|
|
|
| In this example, the entire mouse embryo is disaggregated into cells but the cells are not cultured before use.
|
|
|
|
| cells: "mSCs + mLNCs in BMS activated with anti-Cd3 for 48 hr"
|
|
|
|
| In this example, cells from both the mouse spleens and lymph nodes are mixed.
|
|
|
|
| <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.
|
|
|
|
| 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
|
|
|
|
| note: BMS is used if no description of the medium is given
|
|
|
|
| BSS: balanced salt solution
|
|
|
|
| any conditions that are common to all the samples in the experiment
|
|
|
|
| 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.
|
|
|
|
| In this example, the initial signal is undetectable. The peak response is at 5 min. The signal is decreased by 15 min and undetectable at 60 min.
|
|
|
|
| times: 0++ 30+ 60 120 240+ min
|
|
|
|
| In this example, the initial signal is detectable. The signal decreases at 30 min and is no longer detectable at 60 min. The signal returns at 240 min but is not as strong as the initial signal.
|
|
|
|
| times: 0 1 3+ 5+ 15+ 30+ 60+ min
|
|
|
|
| In this example, the initial signal is undetectable. The signal is detectable by 3 min and stays detectable for up to 60 min.
|
|
|
|
| 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: 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: 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: 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: 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: Protein [KO] | [RNAi] | [AntiSense] | [null-mut]
|
|
|
|
| a positive change is significantly increased in the absence of an endogenous protein
|
|
|
|
| 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: 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
|
|
|
|
| source: PMID-Fig-## or source: PMID-Table-##
|
|
|
|
| source: 9094716-Fig-2e,3b,3e,4c,4d
|
|
|
|
| source: 9020886-Table-1,Fig-3
|
|
|
|
| If the same experiement is done twice, more than figure or table numbers can be used
|
|
|
|
| In some cases, attempts were made to consolidate similar experiments in one datum. This was not a good idea and is in the process of being undone.
|
|
|
|
| This is left over from the days when we tried to make rules from review papers as well as "data" papers. The (D) was used to designate the source as a paper containing data and (R) was used to designate the source as a review or commentary. We are in the process of replacing (D) with figure numbers.
|
|
|
|
|