CTD Dashboard Submission Builder Tutorial And Guidelines
CTD2 Dashboard Submission Builder Tutorial and t/Table of ContentsIntroduction . 2Guidelines for Creating a Dashboard Submission . 2Login. 2Choose the Center . 3Manage Submission . 4Provide Submitter Information and a Submission Description . 4Guidelines to fill in the fields under the Submission Description . 5Provide Submission Data. 6Guidelines for filling in the subject fields . 6Guidelines for filling in the evidence fields . 7Examples to fill in the evidence fields . 8Provide an Observation Summary. 9Download Template. 9Preview the Submission .10References .10
CTD2 Dashboard Submission Builder TutorialIntroductionNetwork Center members share their research findings with the scientific community through theCTD2 Dashboard. Validated, positive results are submitted to the CTD2 Dashboard to allowresearchers to browse results compiled across all the Centers. The intent is threefold : 1) to allowuse of data from multiple Centers to support conclusions, 2) to allow t he discovery of newconnections among the submitted data sets, and 3) to make the findings of CTD 2 Centers easilyavailable to a wider scientific audience. To learn how the Dashboard is organized, includingadditional term definitions, please visit Navigating and Understanding Dashboard Content. Tounderstand more about Dashboard functions, please read the manuscript Aksoy et al.1 or e-Newsarticle Jagu et al.2, or watch the tutorial videos (Organization and Terminology; Search andBrowse; Gene Cart).Note: CTD2 Centers should submit raw or analyzed primary data to the Data Portal. Pleasecontact Subhashini Jagu for questions related to Data Portal submissions.We describe here a web-based interface, known as the “Submission Builder”, to help thesubmitter generate the template for a new submission. There are no links from other CTD 2websites or even from the Dashboard itself to the Submission Builder, as it is meant for the useof submitters from Network Centers only. We request that you do not post links to it on other webpages. A hallmark of the CTD2 Dashboard is that it is general in the kinds of evidence that can besubmitted; hence, the template used to submit data must be customized for each experiment.Since each Dashboard submission is unique, the guidelines we provide for drafting the contentare general and may not apply to all submissions. We suggest submitters review the currentcontent of the Dashboard; it is quite likely that a similar submission has already been made. Thebest suggestion we can provide is that after you write each statement that is part of a submission,ask yourself: Would a cancer researcher unfamiliar with my laboratory’s work be able to understand thisstatement?Have I provided an increasing level of detail from project to description to observationsummary?Is the detail provided sufficient for an outside researcher to learn something substantialby reading it?If you encounter any issues or have questions in preparing a Dashboard submission, pleasecontact Vlado Dancik or Subhashini Jagu.Guidelines for Creating a Dashboard SubmissionLoginThe Dashboard Submission Builder is only available to authorized CTD 2 Center members.Authorized members must have an eRA Commons account; Subhashini Jagu can help insetting-up accounts. When entering the Submission Builder site, you will be redirected to theNIH federated login page. Log in using your eRA Commons credentials and you will beredirected to the Submission Builder “Home” page (Figure 1).2
CTD2 Dashboard Submission Builder TutorialFigure 1: CTD2 Dashboard Submission Builder home page.Choose the CenterSelect the appropriate Center using the pull-down list (Figure 2) and create a template underthe Center name. It is possible to explore templates belonging to other Centers as examples;however, do not create, edit, or delete entries in another Center’s area.Note: In a future version, copying a template from another Center may be implemented toprepare a similar submission from your Center.Figure 2: Submitters select the CTD2 Center using the pull-down menu.3
CTD2 Dashboard Submission Builder TutorialManage SubmissionAfter selecting the Center, you will be directed to the “Manage Submission” page. The newtemplate can either be developed using an existing template from a similar submission, or itcan be created de novo. Either select an existing submission (if the submission underpreparation is similar or related to the pre-existing one) and clone using the pull-down listunder the column Action, or create a new submission ( Figure 3). The fields (SubmissionName, Submission Description, Project, etc.) on this page display information collected duringthe template creation process.Figure 3: Submitters can clone/edit an existing submission using thepull-down list under the column Action or create a new submission byclicking Create New Submission.Provide Submitter Information and a Submission DescriptionIn the appropriate text boxes, provide the submitter’s first name and last name, and a contactemail address and phone number (optional) under “Submitter Information” ( Figure 4).Additionally, provide the submission name, submission description, etc., within the“Submission Description” section. Please see the guidelines below to fill in these fields.Submitters can Save the page to the database or click Save and Continue to proceed to thenext page.Note: Use the Home button to go back to previous pages; the back button on the navigationmenu will direct you back to the Dashboard home page.4
CTD2 Dashboard Submission Builder TutorialFigure 4: Provide the requested information for thesubmitter and submission.Guidelines to fill in the fields under the Submission DescriptionSubmission Name: A Submission is a Dashboard entry that represents a dataset associatedwith positive experimental results, a set of data-related figures, or a story. The submissionname should be short and meaningful and in lower case, without any spaces (use underscoresinstead; e.g., tgen eddy ccle ctrp). It should start with a name or an abbreviation of theCenter and should not exceed 31 characters.Submission Description: The submission description should include names of subject(s) ( e.g.,cancer type, model system, gene, small molecule, etc.) and convey information about theexperimental approach. The summary must not exceed 300 characters.Project Title: In the Dashboard, a “project” is a set of pertinent, interrelated submissionsgrouped together under the same title. The title should provide an overview or snapshot of allsubmissions within the project; it should include a broad goal or conclusion of the project andthe names of subject(s) (e.g., cancer type, model system, gene, small molecule, etc.) if onlyone or a few subjects are the focus of the project. It must not exceed 10 0 characters.Note: Submissions can come from a single Center or multiple Centers for a collaborativeproject. Generally, submissions that are part of a project come from the same publishedmanuscript.Tier: A CTD2 Network-defined ranking system for evidence that is based on the extent ofcharacterization associated with a particular study.o Tier 1: Preliminary results of screening campaignso Tier 2: Confirmation of a subset of primary results in vitroo Tier 3: Validation of a subset of results in a cancer relevant in vivo modelIs this submission a story? A Dashboard story summarizes the research findings from a bigpicture standpoint. Please check the box if the submission is a story and enter the story title.5
CTD2 Dashboard Submission Builder TutorialProvide Submission DataAfter clicking Save and Continue on the “Submission Description” page, you will be directed tothe “Submission Data” page (Figure 5). On this page, you can build a new custom templateor edit an existing template. There are two sections that resemble spreadsheets, one forSubject and one for Evidence. A submission can contain any number of subject(s) and anynumber of associated items of evidence. The page initially displays single rows for subjectand evidence entries. Fill in each row with the appropriate values. Add additional subject andevidence rows by selecting New Subject Row and New Evidence Row as needed. Add a newcolumn for a particular observation associated with the subject and evidence using the NewObservation Column. Multiple observations can be added by adding new rows. Please see theguidelines below to fill in the subject and evidence fields.Note: If a submission has many observations, it will be easier to add them after you havedownloaded the template as an Excel spreadsheet (see “Download Template” to learn howto download the submission).Figure 5: Enter the information associated with the submitted data subjects and evidencepertinent to the submitted data.Guidelines for filling in the subject fieldsSubject: The focus of an experiment or result in a Dashboard submission (e.g., genes,proteins, small molecules, cell lines, animal models).Subject FieldsSubject Class: A Class is a set of objects representing the same molecular or biologicalcategory (DNA, RNA, protein, small molecule, tissue, animal model) and sharing a set ofrequired and optional attributes. Please select the Subject Class (gene, shRNA,tissue sample (disease), cell sample, compound, animal model) using the pull-down menu.6
CTD2 Dashboard Submission Builder TutorialSubject Role: The Center-designated function of a gene, protein, or compound based ontheir 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 perturbagenso biomarker - a gene product or other signal whose presence is an indication of aphenotype or activityo oncogene - a gene known to be involved in causing cancero perturbagen - a substance (small molecule, shRNA, peptide, etc.) designed to disruptintracellular processeso master regulator - a gene for a transcription factor or signaling protein controlling theexpression or repression of a number of direct target geneso candidate master regulator - a master regulator identified in a computational screenbut not yet confirmed in vitroo interactor - a subject involved in an interaction networko background - a subject necessary to understand the importance of the study but notpart of that particular studyo candidate drug - a compound investigated as a potential new drug or for a newindicationo control compound - a compound used as control in an experimento metabolite - product of enzyme-catalyzed reactiono disease - the condition or disease being investigatedo metastasis - spread of cancer cells to new areas of the bodyo tissue - description of tissue used or investigated in an experimento cell line - a cell line used in an experimento strain - strain of an animal modelColumn Tag: Provide a meaningful column tag, which will appear as a column header in thefinal template spreadsheet. Separate words by underscores “ ” and use all lower -case lettersunless 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 bedisplayed on the Dashboard’s website. Each row must have a unique tag (which may includea numeral if multiples are needed (e.g., “gene symbol 1”, “gene symbol 2”)).Description: Enter a description of the subject in the context of the submission in the pop-uptext box, and then click the Close button. You can view the current content (on the observationpage under the Description column in the subject table) of the Dashboard for examples.Observation: Enter the actual subject (e.g., gene symbol for genes, compound name forcompounds, etc.).Guidelines for filling in the evidence fieldsEvidence: Selected positive or validated results from a scientific experiment ( e.g., numericvalues, text labels, data figures).Evidence FieldsValue Type: For each piece of evidence, choose its value type.o numeric - numeric valueo label - value represented as a string or texto file - values or information stored in a fileo url - links to values, information, or resources7
CTD2 Dashboard Submission Builder TutorialEvidence Type: Dashboard evidence types and roles serve as a general way to categorizethe types of evidence in the Dashboard. Select the evidence type after choosing the valuetype of evidence.o measured - directly (experimentally) measured valueso computed - values computed from the datao observed - relevant values that were not measured or computed ( e.g., number ofreplicates)o background - values or information representing additional or implementation detailsabout an observation, for example (background value in parentheses): assay name(TR-FRET), scoring method (RIGER), gene alteration type (mutation), affectedpathway name (glucuronidation), subset of cell lines used (all CCL types), mediatorcriterion (essentiality)o literature - values obtained from literatureo written (applicable to value type file only) - a Dashboard storyo reference (applicable to value type URL only) - a link to a PubMed referenceo resource (applicable to value type URL only) - a link to a website containing resourcesrelevant to an observationo link (applicable to value type URL only) - any other linko species - the type of organism (e.g., mouse, human, etc.) used in the studyColumn Tag: Provide a meaningful column tag, which will appear as a column header in thefinal template spreadsheet. Separate words by underscores “ ” and use all lower -case lettersunless the word is a proper noun or an abbreviation typically styled otherwise ( e.g., DNA).Description: Enter a description of the piece of evidence in the pop-up text box, and thenclick 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 evide nce table) of theDashboard for examples.Observation: Enter the actual value, numeric value, text, or URL link, depending on aselected value type. Upload a file when value type is “file”.Examples to fill in the evidence fieldsReferences: Select “url” as a value type and “reference” as an evidence type, and use“publication reference” as a column tag for listing a reference. Provide first author, title,journal, year, volume, and page numbers under the description, and enter the PubMed URLin the observation column.Figures: Select “file” as a value type and an appropriate evidence type (e.g. measured,observed). Use “figure #” as a column tag, provide under the description a figure legendthat is similar to what would appear in a publication, and upload an image file (preferably inPNG, JPEG, TIFF formats).Note: Make sure that figures and graphs taken directly from the manuscripts adhere to thejournal copyright policies.Evidence Ontology: 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 the8
CTD2 Dashboard Submission Builder Tutorialevidenceontologyterminthedescription and a link toin the observation column.theterm(e.g.,http://w w w.evidenceontology.org/term/ECO:XXXXXX/ )Dashboard Story: Select “file” as a value type and “written” as an evidence type, and use“story location” as a column tag. Use the same description provided under the tab“Submission Description” in the description field.Provide an Observation SummaryAn observation summary is a Center-determined conclusion that is submitted as a connectionbetween subjects and evidence; the observation summary is the “fundamental unit” of theDashboard. The observation summary describes individual observations of the submissionand is built up using the “column tags” as replaceable elements in the text. It should describean experimental outcome or evidence and include qualitative or quantitative details about theconclusion; it may include any additional details for subjects (i.e., mutations or variants used).Clicking the Helper button (Figure 6) provides a list of all the column tags that have beencreated for the current submission. Enter the tags by selecting them in the list, and enter thedescriptive text to complete the observation summary. You can also type text directly into thisfield. When viewed online, the tags will be substituted with individual observation values.Note: The summary must not exceed 300 characters. The text box can be expanded usingthe drag option.Figure 6: Enter the observation summary using the Helper button, which provides thelist of column tags.Download TemplateDownload the completed template as an Excel file. The downloaded Excel spreadshe et hastwo tabs, one for the submission and the other for the associated metadata. You should notedit the content in the cells highlighted in color. For submissions with multiple observations,these can be conveniently added after the template has been downloaded as an Excelspreadsheet.9
CTD2 Dashboard Submission Builder TutorialPreview the SubmissionTo preview the submission, click Save and Continue on the “Observation Summary” page orclick on the Preview option provided under the navigation menu. The Preview shows all thecollected information, including one observation at a time (if any observations have beenentered).Actions: Observation pulldown - if there is more than one observation, select which entry toview from this list.Submission (Show details) - clicking the show details link shows all the informationcollected about the submission.o Description (Details) - this link is not active in the Submission Builder; it works inthe Dashboard itself.o Source Data download - this link is not active in the Submission Builder; it worksin the Dashboard itself, where it can be used to download the complete submissionpackage.Evidence - links under “Details” will not work on the Submission Builder.Note: The Dashboard submission upload process is manual. Hence, submitters must sendthe downloaded Excel spreadsheet to Vlado Dancik for final review and to be uploaded to theDashboard site. The Dashboard team will send a note to the submitter as soon as thesubmission appears live on the site, they should review the submission and let Vlado know ifanything needs to be changed.References1) Aksoy, Dančík, Smith et al. CTD2 Dashboard: a searchable web interface to connectvalidated results from the Cancer Target Discovery and Development Network. Database2017 Aug 8; 2017:1-10. https://www.ncbi.nlm.nih.gov/pubmed/292204502) Jagu et al. CTD2 Dashboard: A Platform to Explore Evidence-based Observations. OCGe-Newsletter, Issue 14: February 2016. er-issue/issue-14#172110
CTD2 Dashboard Submission Builder Tutorial 5 Figure 4: Provide the requested information for the submitter and submission. Guidelines to fill in the fields under the Submission Description Submission Name: A Submission is a Dashboard entry that represents a dataset associated with positive experimental results, a set of data-related figures, or a story.
Use of CTD-Divers at Varying Elevation CTD-Divers can be used at any elevation ranging from 300 meters below sea level to 5,000 meters above sea level. Appendix I contains further information on the use of CTD-Divers at varying elevation. Use in Seawater The CTD-Diver is an excellent choice for use in semi-saline water/seawater. The CTD-Diver has a
3.2. ROC Curve Analysis for Discriminating CTD-ILD from CTD without ILD according to RDW. The RDW was com-pared between the CTD-ILD patients and controls. RDW was higher in the CTD-ILD patients than in CTD patients (14:20 1:45 vs. 13:57 1:38%, p 0:001) (Figure 1(a)). The accuracy of RDW for discriminating CTD-ILD from
ice edge in the Bellingshausen Sea. A few CTD stations were worked on passage. In particular, a line of full-depth CTDs along 88 W was occupied on the final passage leg. This report describes the CTD data collected on that cruise. The CTD system used was that belonging to RVS, comprising a Neil Brown Mark Hlb CTD
of new dashboard, click Zreate New Dashboard [ button on the dashboards view. New Dashboard will be opened in design view, ready to be designed and configured. 3.1. Free Position – Dashboard Layout In this dashboard layout mode, dashboard consist of one area where dashboard tiles (charts) are positioned in any preferred way.
A) Lowering a CTD in a series of vertical "casts." Essential Concept: HTVs can be located by looking for variations in Conductivity, Temperature and Density. Learning Objectives: Students will be able to: explain how data from CTD sensors are used to locate hydrothermal vents. read data from CTD sensors and predict when an HTV is .
prescribed value for different sub-sets of CTD data. ΔS 5 0 Probabilistic approach: historical CTD data Statistics of for different sub-sets of CTD data ΔS 5 0 1446 0.081 0.251 7.8 18224 0.023 0.128 13.1 15695 0.019 0.111 12.4 14190 0.002 0.007 6.4 Std skew (psu) Mean (psu) No. of profiles Group σ 5 0 σ 10 5 σ 10 5 T .
Obtain stakeholder information about the needs, challenges, investments necessary to implement the CTD and eCTD format. The Agency will use this information to plan the necessary transition time (voluntary adoption of the CTD and eCTD format) and ways to assist industry to achieve total adoption of the CTD and eCTD format.
00_Crawford_Price_BAB1407B0153_Prelims.indd 1 11/11/2014 7:36:56 PM. 1 INTRODUCING GROUPWORK Chapter summary In this chapter you will learn about the overall purpose, aims, scope and features of this book how the book is structured and the brief contents of each chapter how the book is aligned with a range of national standards and requirements related to professional social work .
