Please add a little question mark circle next to the following title headings under Submission Data:
-- Subject
-- Subject Class
-- Subject Role
-- Column Tag
-- Description
-- Observation
-- Evidence
-- Value Type
-- Evidence Type
-- Column Tag
-- Description
-- Observation
Then, as the user hover overs the question marks, please provide the following corresponding definitions:
-- For Subject: "The focus of an experiment or result in a Dashboard submission (e.g., genes, proteins, small molecules, cell lines, animal models)."
-- For Subject Class: "A Class is a set of objects representing the same molecular or biological category (DNA, RNA, protein, small molecule, tissue, animal model) and sharing a set of required and optional attributes. Please select the Subject Class (gene, shRNA, tissue_sample (disease), cell_sample, compound, animal_model) using the pull-down menu."
-- For Subject Role: "The Center-designated function of a gene, protein, or compound based on their interpretation of observations within a particular experimental or computational context.
Note: Select the role from the below restricted list of terms under the pull-down menu.
o target - a gene or protein targeted by chemical or genetic perturbagens
o biomarker - a gene product or other signal whose presence is an indication of a phenotype or activity
o oncogene - a gene known to be involved in causing cancer
o perturbagen - a substance (small molecule, shRNA, peptide, etc.) designed to disrupt intracellular processes
o master regulator - a gene for a transcription factor or signaling protein controlling the expression or repression of a number of direct target genes
o candidate master regulator - a master regulator identified in a computational screen but not yet confirmed in vitro
o interactor - a subject involved in an interaction network
o background - a subject necessary to understand the importance of the study but not part of that particular study
o candidate drug - a compound investigated as a potential new drug or for a new indication
o control compound - a compound used as control in an experiment
o metabolite - product of enzyme-catalyzed reaction
o disease - the condition or disease being investigated
o metastasis - spread of cancer cells to new areas of the body
o tissue - description of tissue used or investigated in an experiment
o cell line - a cell line used in an experiment
o strain - strain of an animal model"
-- For Column Tag: "Provide a meaningful column tag, which will appear as a column header in the final template spreadsheet. Separate words by underscores “_” and use all lower-case letters unless the word is a proper noun or an abbreviation typically styled otherwise (e.g., DNA). The column tag is used internally to populate the observation summary and will not be displayed on the Dashboard’s website. Each row must have a unique tag (which may include a numeral if multiples are needed (e.g., “gene_symbol_1”, “gene_symbol_2”))."
-- For Description: "Enter a description of the subject in the context of the submission in the pop-up text box, and then click the Close button. You can view the current content (on the observation page under the Description column in the subject table) of the Dashboard for examples."
-- For Observation: "Enter the actual subject (e.g., gene symbol for genes, compound name for compounds, etc.)."
-- For Evidence: "Selected positive or validated results from a scientific experiment (e.g., numeric values, text labels, data figures)."
-- For Value Type: "For each piece of evidence, choose its value type.
o numeric - numeric value
o label - value represented as a string or text
o file - values or information stored in a file
o url - links to values, information, or resources"
-- For Evidence Type: "Dashboard evidence types and roles serve as a general way to categorize the types of evidence in the Dashboard. Select the evidence type after choosing the value type of evidence.
o measured - directly (experimentally) measured values
o computed - values computed from the data
o observed - relevant values that were not measured or computed (e.g., number of replicates)
o background - values or information representing additional or implementation details about an observation, for example (background value in parentheses): assay name (TR-FRET), scoring method (RIGER), gene alteration type (mutation), affected pathway name (glucuronidation), subset of cell lines used (all CCL types), mediator criterion (essentiality)
o literature - values obtained from literature
o written (applicable to value type file only) - a Dashboard story
o reference (applicable to value type URL only) - a link to a PubMed reference
o resource (applicable to value type URL only) - a link to a website containing resources relevant to an observation
o link (applicable to value type URL only) - any other link
o species - the type of organism (e.g., mouse, human, etc.) used in the study
Annotate evidence types using the Evidence Ontology as a reference. Select “url” as a value type, select “link” as an evidence type, and use “evidence_ontology_term” as a column tag under the evidence. Then provide the evidence ontology term in the description and a link to the term (e.g., http://www.evidenceontology.org/term/ECO:XXXXXX/) in the observation column."
-- For Column Tag: "Provide a meaningful column tag, which will appear as a column header in the final template spreadsheet. Separate words by underscores “_” and use all lower-case letters unless the word is a proper noun or an abbreviation typically styled otherwise (e.g., DNA)."
-- For Description: "Enter a description of the piece of evidence in the pop-up text box, and then click the Close button. HTML markup can be also included. You can view the current content (on the observation page under the Description column in the evidence table) of the Dashboard for examples."
-- For Observation: "Enter the actual value, numeric value, text, or URL link, depending on a selected value type. Upload a file when value type is “file”."
Please add a little question mark circle next to the following title headings under Submission Data: -- Subject -- Subject Class -- Subject Role -- Column Tag -- Description -- Observation -- Evidence -- Value Type -- Evidence Type -- Column Tag -- Description -- Observation
Then, as the user hover overs the question marks, please provide the following corresponding definitions:
-- For Subject: "The focus of an experiment or result in a Dashboard submission (e.g., genes, proteins, small molecules, cell lines, animal models)."
-- For Subject Class: "A Class is a set of objects representing the same molecular or biological category (DNA, RNA, protein, small molecule, tissue, animal model) and sharing a set of required and optional attributes. Please select the Subject Class (gene, shRNA, tissue_sample (disease), cell_sample, compound, animal_model) using the pull-down menu."
-- For Subject Role: "The Center-designated function of a gene, protein, or compound based on their interpretation of observations within a particular experimental or computational context. Note: Select the role from the below restricted list of terms under the pull-down menu. o target - a gene or protein targeted by chemical or genetic perturbagens o biomarker - a gene product or other signal whose presence is an indication of a phenotype or activity o oncogene - a gene known to be involved in causing cancer o perturbagen - a substance (small molecule, shRNA, peptide, etc.) designed to disrupt intracellular processes o master regulator - a gene for a transcription factor or signaling protein controlling the expression or repression of a number of direct target genes o candidate master regulator - a master regulator identified in a computational screen but not yet confirmed in vitro o interactor - a subject involved in an interaction network o background - a subject necessary to understand the importance of the study but not part of that particular study o candidate drug - a compound investigated as a potential new drug or for a new indication o control compound - a compound used as control in an experiment o metabolite - product of enzyme-catalyzed reaction o disease - the condition or disease being investigated o metastasis - spread of cancer cells to new areas of the body o tissue - description of tissue used or investigated in an experiment o cell line - a cell line used in an experiment o strain - strain of an animal model"
-- For Column Tag: "Provide a meaningful column tag, which will appear as a column header in the final template spreadsheet. Separate words by underscores “_” and use all lower-case letters unless the word is a proper noun or an abbreviation typically styled otherwise (e.g., DNA). The column tag is used internally to populate the observation summary and will not be displayed on the Dashboard’s website. Each row must have a unique tag (which may include a numeral if multiples are needed (e.g., “gene_symbol_1”, “gene_symbol_2”))."
-- For Description: "Enter a description of the subject in the context of the submission in the pop-up text box, and then click the Close button. You can view the current content (on the observation page under the Description column in the subject table) of the Dashboard for examples."
-- For Observation: "Enter the actual subject (e.g., gene symbol for genes, compound name for compounds, etc.)."
-- For Evidence: "Selected positive or validated results from a scientific experiment (e.g., numeric values, text labels, data figures)."
-- For Value Type: "For each piece of evidence, choose its value type. o numeric - numeric value o label - value represented as a string or text o file - values or information stored in a file o url - links to values, information, or resources"
-- For Evidence Type: "Dashboard evidence types and roles serve as a general way to categorize the types of evidence in the Dashboard. Select the evidence type after choosing the value type of evidence. o measured - directly (experimentally) measured values o computed - values computed from the data o observed - relevant values that were not measured or computed (e.g., number of replicates) o background - values or information representing additional or implementation details about an observation, for example (background value in parentheses): assay name (TR-FRET), scoring method (RIGER), gene alteration type (mutation), affected pathway name (glucuronidation), subset of cell lines used (all CCL types), mediator criterion (essentiality) o literature - values obtained from literature o written (applicable to value type file only) - a Dashboard story o reference (applicable to value type URL only) - a link to a PubMed reference o resource (applicable to value type URL only) - a link to a website containing resources relevant to an observation o link (applicable to value type URL only) - any other link o species - the type of organism (e.g., mouse, human, etc.) used in the study
Annotate evidence types using the Evidence Ontology as a reference. Select “url” as a value type, select “link” as an evidence type, and use “evidence_ontology_term” as a column tag under the evidence. Then provide the evidence ontology term in the description and a link to the term (e.g., http://www.evidenceontology.org/term/ECO:XXXXXX/) in the observation column."
Please hyperlink 'Evidence Ontology' above with: http://www.evidenceontology.org/ Also, please hyper link 'evidence ontology term above with: http://www.evidenceontology.org/browse/
-- For Column Tag: "Provide a meaningful column tag, which will appear as a column header in the final template spreadsheet. Separate words by underscores “_” and use all lower-case letters unless the word is a proper noun or an abbreviation typically styled otherwise (e.g., DNA)."
-- For Description: "Enter a description of the piece of evidence in the pop-up text box, and then click the Close button. HTML markup can be also included. You can view the current content (on the observation page under the Description column in the evidence table) of the Dashboard for examples."
-- For Observation: "Enter the actual value, numeric value, text, or URL link, depending on a selected value type. Upload a file when value type is “file”."