ORF View (GO)

Menus available when an ORF RECORD is open in the Board

Fields

Note

Lab Visible Only

This can be set to allow only the lab that owns the record to see it.

  1. To set it, go to ORF, Lab Visible Only, and check or uncheck the box in the pop-up as desired.
  2. This setting is saved to the database when 'OK' is clicked.

Create ORF

ORF records can be created in four ways and can be done by lab masters or anyone given the 'Can Do'.
  1. Singly, from a blank 'Create ORF' form.
    • To make this function available, SearchORF (GO) → By List (Board), entering '0' into the List field. Alternatively, search for any ORF but do not select it; if an ORF is selected by error it can be deselected by EditClear Selection.
    • In the ORF(s) menu choose Create ORF, fill in fields as necessary, and click the Create ORF button at the bottom of the pop-up.
  2. Singly, using an existing ORF record as a template.
    • SearchORF (GO) → By List (Board), entering the number of the template ORF into the search box.
    • Select the template ORF in the list that appears in the Board.
    • In the ORF(s) menu choose Create ORF, make any alterations needed to the pop-up, and click the Create ORF button at the bottom of the pop-up.
  3. Singly, from a Target Request record.
    • Make a completed Target Requestrecord active in the Board.
    • In the Target Request menu click Create ORF.
    • A pop-up containing information taken from theTarget Request record will appear. Content can be added, deleted, or altered in various fields at this point. To then create the ORF record, press the Create ORF button at the bottom of the pop-up.
  4. One or more at a time, using the Bulk Load function described in Lab Resources Bulk Load

Note

Create ORF Variants

ORF records with sequence-truncated or sequence-extended versions of existing ORFs can be created using the ORF Surgery Function. This function can be used by lab masters and those who have a 'Can Do'.
  1. Create an ORF Surgery item specifying the sequence truncations or additions to be made, as described in Lab Resources ORF Surgery List.
  2. Search for the 'parent' ORF (the sequence to be truncated or extended) by SearchORFBy List (Board).
  3. Highlight the 'parent' ORF in the Board list by clicking on it.
  4. In the ORF(s) menu, choose Create ORF Variants.
  5. Choose the ORF Surgery item from the ORF Surgery List dropdown.
  6. Set Visibility as desired.
  7. Click 'Create'.

Note

Refresh ORF

This reverts the data in the ORF record to the version in the database.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Refresh ORF.

Close ORF

This closes the window.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Close ORF, or click the X button on the window's Title bar.

Note

Show All Cells

This shows all Fields, including the hidden ones, in the ORF view.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Show all Cells.

Note

Show Lab Visible Cells

This hides the originally hidden Fields in the ORF view; i.e., any fields hidden by a lab master, then revealed by Show all Cells, will again be hidden.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Show Lab Visible Cells.

Save ORF Info

This saves new entries in the ORF Info field in the database.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Save ORF Info.

Save TT Elements

This saves to the database content entered into the TargetTrack fields 'TT Target Rationale' and 'TT Target Annotations.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Save TT Elements.

Save External References

This saves to the database content entered into the External References field.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Save TT Elements.

Set ORF Lab Only

This makes the ORF visible only to the User's lab.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Set ORF Lab Only.

Delete ORF

This removes the ORF from the database.

  1. Make the ORF window active in the Board.
  2. On the ORF menu click Delete ORF.
  3. If you are sure you want to remove the ORF from the database, Click OK.

Note

Generate Report for ORF

This creates a text report of the information in the ORF record.

  1. Make the ORF window active in the Board.
  2. In the Report menu click Generate Report for ORF.

Note

Record XML Dump

This saves an XML report for the ORF to the disk.

  1. Make the ORF window active in the Board.
  2. In the Report menu click Record XML Dump.
  3. Fill out the pop up.
    • Inline DTD determines if the DTD (Document Type Definition) should be included in the file.
    • Formatting determines if newlines and spaces should be included in the file.
    • File Name defines the name of the file to be saved.
  4. Click the Save File button.

Note

Get Genealogy

This creates a genealogy or 'tree' consisting of all records to which an ORF is linked as well as the Protocol attached to each, enabling one to trace its path through a pipeline.

  1. Make the ORF window active in the Board.
  2. 2. In the Report menu click Get Genealogy.

TT Trials

This creates a list of attempts (trials, as defined for the Protein Structure Initiative Target Track database ) to produce the protein encoded by an ORF. The output includes, among much other information, all actions applied to an ORF during each trial.

  1. Make the ORF(s) window active in the Board.
  2. Go to ReportTT Trials
  3. Choose a Labfund from the pop-up to specify the project or organization under which the work would have been done.
  4. Click the Report button.

Set ORF(s) Lab Only

This makes the ORF(s) visible only to the User's lab.

  1. Make the ORF(s) window active in the Board.
  2. On the ORF(s) menu click Set ORF(s) lab only.

Delete ORF(s) from DB

This removes the ORF(s) from the database.

  1. Make the ORF(s) window active in the Board.
  2. On the ORF(s) menu click Delete ORF(s).
  3. If you are sure you want to remove the ORF(s) from the database, Click OK.

Note

Add to Search Results

This adds ORFs selected from the List to search results in the main window; equivalent to double-clicking on an ORF in a list.

  1. Select ORF(s) from the ORF List by clicking on them.
  2. In the ORF(s) menu select Add to Search Results.

Show/Hide Columns

This hides data columns in the ORF list or returns those that were previously hidden.

  1. In the ORF(s) menu select Show/Hide Columns.
  2. In the pop-up, deselect columns you wish to hide and click Set.
  3. To return columns to view, in the ORF(s) menu select Show/Hide Columns, select those that you wish to see, and click Set.

Update ORF

This allows the Sesame Administrator to update information in ORF fields and is inactive for anyone else.

Create Protein Records

This creates Protein (LA) records based on information in a listed ORF record and information selected in a pop-up.

  1. Select an ORF or ORFs from a list resulting from a search or a list in a Workgroup record.
  2. In the ORF(s) menu select Create Protein Records.
  3. The pop-contains the following fields:
    • Labfund is a drop-down list of various sources of funding maintained by the lab master.
    • Status is a drop-down list of Protein record Status choices maintained by the lab master.
    • Type is a drop-down list of Protein record Type choices maintained by the lab master.
    • User Label is an additional label for the Protein.
    • Add Workgroup Path to User Label places the identifiers of workgroups leading to the Protein record in the User Label field; however, there is no input when creating a Protein record from an ORF record.
    • Room is a drop-down list of room location choices maintained by the lab master.
    • Freezer is a drop-down list of freezer location choices maintained by the lab master.
    • Shelf is a drop-down list of shelf location choices maintained by the lab master.
    • Tower is a drop-down list of tower location choices maintained by the lab master.
    • Box is a drop-down list of box location choices maintained by the lab master.
    • ORF main id to Protein name is a checkbox to allow the content of the ORF Main ID field of the ORF record to be carried over to the Protein Name field of the Protein record.
    • ORF lab id to Protein name is a checkbox to allow the content of the ORF Lab ID field of the ORF record to be carried over to the Protein Name field of the Protein record.
    • Lab Protocol is a drop-down menu of Lab Protocols that can be selected for application to the new Protein record. The list is maintained by the lab master.
    • Determine Cleaved Sequence is a checkbox to allow formulation of the cleaved protein sequence and placement into the new Protein record. This function takes into account (1) Any differences from the model sequence in the ORF record determined by the lab and placed in a linked Plasmid record, (2) Any changes to the model sequence in the ORF record made during cloning into a particular vector, based on the vector chosen from a list that becomes available in the Expression Vector field after a Lab Protocol is selected.
    • Determine Uncleaved Sequence is a checkbox to allow formulation of the uncleaved (tag-on) protein sequence and placement into the new Protein record. This function takes into account (1) Any differences from the model sequence in the ORF record determined by the lab and placed in a linked Plasmid record, (2) Any changes to the model sequence in the ORF record made during cloning into a particular vector, based on the vector is chosen from a list that becomes available in the Expression Vector field after a Lab Protocol is selected, (3) the tag or tags added to the ORF record model sequence through expression from a particular vector, based on the vector is chosen from a list that becomes available in the Expression Vector field after a Lab Protocol is selected.
    • Expression Vector is a drop-down list of protein expression vectors that appears after a Lab Protocol is chosen.
    • Labeling is the type of labeling, eg. SeMet 100%.
    • Protocol is the Protocol Tree defined with the Protocol selected in the above Lab Protocol field.

Note

Create Sample Records

Search By ID

  1. Open the 'Search By ID' popup.
    • In the Search menu, choose By ID
  2. Set the search criteria in the 'Search By ID' popup.

Note

Search By External Reference

Note

To view an ORF, double-click on a row in the ORF(s) List, or drag and drop a row from the ORF(s) View to the Board. The ORF record will be shown in the Board.

Search By Content

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Search By Criteria

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Search By Action

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Search By Characteristics

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Search By List

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Search By Linked Item List

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Search By Sequence

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See also