Shortlist and export

The shortlist

The Shortlist region keeps references and hits together for a case. It says what it is: "A working list of references and hits kept together for this case. Being on the shortlist is not a finding, not evidence, and not a decision on a reference; changes are recorded in the log below and never overwrite an earlier version."

• Add to shortlist is offered in an open reference, for the reference and each of its hits, and beside each identity hit not rolled up to a reference. You can give a reason: "At most 2,000 characters. The reason is shown to everyone who can view this case and is included in a shortlist export."
• Remove from shortlist takes an item off. "Removed from the shortlist. It stays in the log."
• Each item shows its current state, for example "No longer in the current roll-up" when a later roll-up no longer holds it. An item is never removed for you.
• Shortlist version reads an earlier version: "Reading an earlier version shows the members at that version; it changes nothing."
• Show the log of changes opens "Changes to the shortlist, newest first": every change, with who made it and why.

"Only the case examiner or the searcher who entered the case changes the shortlist." A shortlist holds at most 500 items.

Export

Three exports share one dialog: Export results… on a search's result page, Export shortlist… on the shortlist, and Export the record… in the Summary region. "Choose a format, a saved template of fields and a redaction profile. The file lists the shortlist members at the version shown. Nothing is chosen for you."

• Format: CSV (comma-separated values), JSON, XML, FASTA (aligned residues) or PDF (tagged document). PDF exports are tagged, and they make no PDF/UA-1 conformance claim.
• Template: "A file always carries the fields of a saved template. Built-in templates are listed first." You choose the fields under Fields; fields marked "Always included" cannot be left out. Save as new template keeps your choice of fields.
• Redaction profile: the redaction profile, described below.

Every export ends with a receipt, "Export receipt", that gives the content digest and how many values were withheld. An export holds at most 5,000 rows and 9 MB.

Redaction profiles

Every export passes through one redaction stage. There are two profiles to choose from.

• Mark with the configured CUI designation (cui_basic_v1): "Nothing is withheld. The file is marked with the designation this deployment is configured with." The marking comes only from a designation your deployment is configured with. None is set by default, so until one is configured this profile is shown as unavailable, with the reason.
• Redact for a recipient (recipient_v1): you choose the recipient, inside or outside the examining office. For a recipient inside it, nothing is withheld. For a recipient outside it, these are withheld: unpublished references, case-identifying text, own-filing identifiers and counts, imported text, residues, free text and record text. Each withheld value is replaced by a marker that names its class.

After each export is rendered, a check looks for any withheld value in it. If one appears, nothing is exported.

Limits

• Which records were found is not withheld, because an identity hit can disclose the searched sequence. The dialog and every export say so, under "A limit of every export".
• A FASTA file has no place for a marking or a license line. It is made for a recipient inside the examining office only. When your deployment has a CUI designation, or the file holds a sequence from a database that requires attribution (UniProtKB/Swiss-Prot), it arrives as a .zip holding a notice, the FASTA file and a manifest. A FASTA of patent-database sequences only is a plain .fasta file.
• The result-set, shortlist and case record exports name the attribution each database searched requires, such as "UniProtKB/Swiss-Prot, © The UniProt Consortium, CC BY 4.0". A result-set export also names the releases searched, when the search recorded them.
• Every export, including the export of selected searches from My searches, passes through the redaction stage.
• "Only the case examiner or a supervisor exports. The searcher who entered the case can view the shortlist but not export it."