Use Protocol Chat

What this is

Protocol Chat lets you ask questions about a project's study documents and get answers that cite the document and page they came from. You upload a PDF to a project, Sitebase reads it page by page, and you can then ask it questions in plain language. Every statement in an answer links to the passage it is based on, so you can check it against the document in one click.

When you upload a Protocol, Sitebase also extracts a structured summary of the study. Setting up a study from a protocol is coming soon.

Protocol Chat appears in two places in the sidebar:

• Document chat, under the organization's pages, covers every project you can access. Use it to move between projects or to see all of your chats and saved responses in one place.

• Chat, under the selected project, covers only that project's documents, chats, and saved responses.

Both open the same pages. The left column of each has New chat, Chats, Documents (in a project) or Projects (in Document chat), Study responses, any documents being processed, and Recents, your most recent chats.

When to use it

• You need to check what the protocol says about eligibility, a visit, a procedure, or consent, and want the page reference.

• You want to keep checked answers to common questions so you can find them again later.

• A new protocol version or amendment has arrived and you want chat to answer from it.

Before you start

• Within Protocol Chat, each action also needs its own permission on the project or organization:

  • Viewing the documents and opening Protocol Chat needs permission to list documents.

  • Uploading documents and new versions needs permission to add documents. Without it, Upload document does not appear.

  • Archiving and restoring documents needs permission to delete documents. Without it, Archive document does not appear.

  • Asking questions, rating and saving answers, and archiving chats need permission to create chats. Without it, the question box is disabled.

• Have your document as a PDF of up to 50 MB. Text-based PDFs work best, because Sitebase cites passages by finding their text on the page.

Upload a document

1. Click Chat in the project section of the sidebar, then click Documents in the left column. You can also click Upload document from Document chat or the Chats page.

2. Click Upload document, or drag a PDF onto Drop a PDF here. The Add a document dialog opens.

3. Under Project, choose the project the document belongs to. Only projects you can upload to are listed. The document is visible only within this project, and chats about it live in this project.

4. Click Upload a new PDF and choose the file.

5. Under What kind of document is this?, choose the document type. The type decides what Sitebase does with the file and cannot be changed after upload:

   • Protocol: for a study protocol or amendment. Sitebase indexes every page for chat, and also extracts a structured summary of the study. If Sitebase cannot extract a study from the file, it shows "This file can't be used as a protocol." Upload it as Other document instead.

   • Other document: for ICFs, manuals, charters, and SOPs. Sitebase indexes every page for chat only. There is no structured summary.

   The upload starts as soon as you choose a type, and the dialog closes.

6. Watch the left column. Under Processing, the document shows "Uploading…", then "Extracting text…". You can keep working while it processes, which can take several minutes. A spinner beside Chat in the sidebar shows that documents are processing.

7. When processing finishes, Sitebase shows "A document in [project] is ready" with an Open button, and the document moves to Ready to open, with the note "Ready for chat. Every page can be cited." The sidebar shows how many documents are ready to open.

8. On the Ready to open card, choose what to do next:

   • Start chatting opens a new chat about this document.

   • Dismiss removes the card from the left column. The document stays in the project.

If processing fails, Sitebase shows "A document in [project] couldn't be read", and the document's card shows Extraction failed with a reason. Archive it and upload the file again, or upload a text-based version of the PDF.

Use a document that is already in Sitebase

The Add a document dialog also lists the documents already in the selected project, under Documents in this project. Click one to open a new chat about it instead of uploading a copy.

If documents exist in your other projects, click From other projects to see them. Clicking one opens a new chat in that document's own project. It does not copy the document into the project you selected.

Ask a question

1. Click Chat in the project section of the sidebar. The page "Ask about [project]" opens. You can also start from Document chat, which covers every project you can access.

2. Check the document chip in the question box. Each chat reads one document, and the chip shows which one. It starts on the most recent finished Protocol, or, if there is none, the most recent finished document.

3. Optional: To ask about a different document, click the chip, point to a project, and choose one of its documents. A project with no documents opens the upload for it, and Upload a document at the bottom of the menu adds a new one.

4. Type your question in Ask [document] anything… and press Enter or click Send. You can also click one of the suggestions under the box: What are the I/E criteria?, What happens at the screening visit?, or What needs to happen before consent?

   A new chat opens and asks your question. The first question becomes the chat's title.

5. Wait while "Reading the documents…" shows. Click Stop if you want to cancel the answer.

6. Read the answer. Each statement has a marker for the passage it is based on. Under the answer, Sources lists every page the answer cites, such as p.12 or p.12 · §5.1. If no passage in the document supports the answer, it shows "No passage supports this", and you should not rely on that answer.

7. Click a statement's marker or a page under Sources to open the document on the right at that page, with the cited passage highlighted.

8. Ask a follow-up question in Ask a question about these documents…, or start a New chat for an unrelated topic.

Questions can be up to 4,000 characters. Answers come only from the document the chat reads. If the document does not cover a question, the answer says so.

Start a chat about a specific document

Besides the document chip on the Chat page, you can start from the document itself:

• On the Documents page, click Ask on the document's card.

• On a document's Ready to open card, click Start chatting.

Each of these opens a new chat that reads only that document.

Switch the document a chat reads

1. In the chat, click the document chip at the left of the question box, which shows the number of documents.

2. Under Documents in this chat, check a different document. Only documents that have finished processing can be checked.

The chat switches to the checked document, and later answers come only from it. Earlier answers keep their citations to the previous document. A chat must always read a document, so you cannot uncheck the only one. Sitebase shows "A chat needs at least one document" if you try.

Act on an answer

Each answer has these actions underneath it:

• Save to study responses keeps the answer, with its citations, on your Study responses page. The button changes to Saved. Click Saved to remove it again. Saved responses are personal to you; other users do not see them.

• Copy copies the answer as plain text, with each citation written as its page in brackets, such as (p.12), so you can paste it into an email or a note.

• Helpful records that the answer was right.

• Not right records that the answer was wrong. The answer is flagged for review and sent to the extraction team with its passages, so they can improve how documents are read. Sitebase shows "Flagged for review. Sent to the extraction team with its passages."

You can change a rating from Helpful to Not right or back, but you cannot clear it once set.

If an answer could not be written, the chat shows "This answer couldn't be produced." Click Ask again.

Use the document panel

The right side of a chat shows the document the chat reads. Click the panel icon at the top of the chat to hide or show it. Drag the divider between the chat and the document to resize them. Sitebase remembers the split, and double-clicking the divider resets it to half and half. The panel has these tabs:

The More actions menu (the three dots beside the document) offers:

• Upload new version: adds a new version of this document. See Upload a new version below.

• Open PDF in new tab and Download: open or save the original PDF.

• Remove from this chat: takes the document out of this chat only. It stays in the project and in other chats.

• Archive document: takes the document out of the project and out of every chat. See Archive and restore a document below.

Find and manage your chats

Chats are personal. You see only the chats you started, and other users cannot open them.

1. Click Chats in the left column. Your chats are listed together, with how many there are, the document each one reads, the number of questions, and when it was last updated.

2. Type in Search chats to find a chat by its title or by the document it reads.

3. Optional: Use Project to show one project's chats, or All projects to show them all.

4. Optional: Use Sort to order the list by Most recent, Oldest first, Title A–Z, or Project.

5. Click a chat to reopen it. Your most recent chats are also listed under Recents in the left column.

Archive a chat

Archive a chat to take it out of your chat list without losing it.

1. On the Chats page, click the archive icon on the chat.

2. Sitebase shows "Chat archived" with an Undo button.

An archived chat keeps its questions, answers, and any study responses saved from it. It moves to the archived section at the bottom of the Chats page, shown as the number of archived chats. When you open it, it is read-only: the question box is replaced by "This chat is archived, so it is read-only. Restore it to ask more." Click Restore in that message, or beside the chat in the archived section, to bring it back to your list and ask again.

Manage a project's documents

The Documents page lists every document in the project and the chats in it. Each card shows the document's type (Protocol or Other), its status, and, when it is ready, its version, page count, and how many chats read it.

Upload a new version

Use this when a protocol is amended or a manual is updated, so chats answer from the current version.

1. On the document's card, or in a chat's document panel, click More actions > Upload new version.

2. In Upload a new version of [document], choose the new PDF. The upload starts straight away, with the same document type as the original.

When the new version has been read, every chat that reads the document answers from it. Chats always read a document's most recent finished version, so a version that is still processing or that failed does not replace the one before it. Answers given before the new version keep their citations to the old one.

Archive and restore a document

Archiving a document affects every user in the project, so check before you archive.

1. On the document's card, or in a chat's document panel, click More actions > Archive document.

2. Sitebase shows "[document] archived" with an Undo button.

Archiving a document:

• Archives every version of it.

• Takes it out of the project's document list and out of every chat that reads it, including other users' chats. A chat that read only this document shows "This chat has no documents" until a document is checked in its question box.

Archived documents are listed at the bottom of the Documents page, shown as the number of archived documents. Click Restore beside one to return it to the project. Restoring does not put it back into the chats it was taken out of. To use it in a chat again, start a new chat with Ask, or check it in an existing chat's question box.

Review study responses

A study response is a chat answer you saved with Save to study responses. It keeps its document and page citations, so you can build your own list of checked answers to common questions.

1. Click Study responses in the left column. In Document chat, the page shows your saved responses from every project. In a project's Chat, it shows only that project's.

2. If your responses come from more than one project, click a project to show only its responses, or All projects to show them all.

3. Click a response to open the chat it came from, with its citations. A response whose answer cites no passage shows No citations and the document its chat read.

4. To remove a response, click its X (Remove from study responses). Sitebase shows "Removed from study responses". This removes the saved copy only; the answer stays in its chat.

Study setup

Study setup is coming soon. It will use an uploaded Protocol to propose how the study is set up, including its design, arms and epochs, visits and schedule, pre-screener, inclusion and exclusion criteria, participant statuses, edit checks, rules, notifications, and randomization. Each proposal will link to the passage in the protocol it came from, so it can be checked against the source before it is used.

Messages you may see

Tips

• Check the cited passage before you rely on an answer, especially for eligibility decisions. Click the page under Sources to read it in context.

• Each chat reads one document. To ask about a consent form or manual in a project that has a protocol, choose it in the document chip before you ask, or start the chat with Ask on that document's card.

• Upload amendments with Upload new version rather than as a new document, so existing chats move to the current version and the project does not hold two copies.

• Mark wrong answers Not right, so the extraction team can review them with their passages.

• Save answers to questions you get often, such as visit windows or exclusion criteria, so you can find them on Study responses without asking again.

Still need help? Submit a help request here.