Help
Help & guides
How each stage works, what the checks mean, and what to do when something stops.
All topics
Getting started
What a project is, how to create one, and the settings every later stage follows.
- Getting started in FoodProt AI2 minWhat a project is, what the study configuration sets, and the order the stages run in.
- Creating a project1 minWhat you choose when you create a project, what happens automatically, and what to do first.
- Writing a clear study configuration2 minCriteria that a colleague and the platform apply the same way, and target units chosen before extraction.
- Your first project in five minutes1 minThe shortest path from an empty project to one value shown beside its evidence.
- The six stages, end to end2 minWhat each stage does, and the usual reasons a stage stops and waits.
Finding literature
Searching the databases the platform can search for you, importing from the others, and removing duplicates.
- Searching the literature6 minWhich databases are searched for you, which you search yourself, and what each search records.
- Importing reference files3 minBringing in papers by DOI or PubMed ID, from a pasted reference list, or from RIS, BibTeX, CSV and Excel files.
- The library3 minFind, star, select, organise, read and export the papers of a project.
- Removing duplicates1 minHow duplicate papers are found, and why every merge waits for your confirmation.
- Database coverage2 minWhich databases can be searched for you, what each one always or only sometimes returns, and which must be imported instead.
Screening and prioritisation
Deciding which papers are in scope, then ordering them by how likely they are to contain data.
Full text
Getting full text by legal routes, uploading PDFs yourself, and matching files to papers.
- Getting full text, legally1 minHow full text is found automatically, what the platform will not fetch, and how the manual list works.
- Uploading PDFs yourself1 minHow an uploaded file is matched to a paper, when the match is automatic, and what happens with duplicate files.
- Matching unmatched PDFs1 minWhy a file lands in the unmatched list, how to attach it, and what to check first.
- Using your library access2 minWhat happens when a paper is behind a paywall your institution subscribes to, and what the platform does and does not do.
Understanding documents
Reading the structure of a PDF, recognising the terms in it, and reviewing the vocabulary.
- Reading the structure of a PDF (parsing)1 minWhat parsing produces, why a person checks it before anything else uses it, and what the warnings mean.
- Recognising terms in a paper1 minHow the names of proteins, properties and treatments are found in a paper and matched to the project vocabulary.
- Reviewing the vocabulary (ontology)1 minShared terms, project terms and synonyms, and why outside identifiers are never made up.
Evidence and measurements
Turning papers into values linked to their evidence, checking them, and approving them.
- Extracting values1 minHow candidate values are read from approved documents, what each one carries, and why a candidate is not yet data.
- Figures and tables2 minTables are read from their cells, plots are measured against their own axes, and every value read from a figure is reviewed by a person.
- Quality checks1 minFixed rules, three levels of flag, and why open warnings also hold a value back.
- Reviewing extracted values1 minHow to read a candidate value, the four review decisions, and who can give final approval.
- The verified dataset1 minWhat a verified value is, how the dataset is organised, and how to filter it.
- Units and standardisation1 minHow units are standardised: the reported value is kept beside the converted one, and unsafe conversions are refused.
- Method conditions and units6 minA number means little without its method: which method a value was measured by, which conditions must be reported, and why missing ones are never filled in.
- Confidence, thresholds and abstention2 minWhat a confidence number means, how thresholds decide who looks at what, and why the platform sometimes gives no answer.
Dataset, validation and exports
Checking accuracy against a reference set built by hand, and exporting a dataset others can check.
- Exports and the audit trail1 minWhat the FoodProt AI export contains, who can export, and what the provenance columns let a reader check.
- Handing a dataset to FoodProt2 minFoodProt AI and the FoodProt database are two separate products. What moves between them, how, and what does not.
- Scientific validation1 minMeasuring accuracy against a reference set built by hand, with example sets kept separate from real ones.
- Importing spreadsheets and existing data1 minBringing in legacy FoodProt sheets and hand-collected data, with every column confirmed by you.
Analysing and writing
Working with the data in a workbook, and writing a manuscript with citations from your library.
- Reading, searching and annotating a PDF2 minOpen a paper beside its details, find words in it, highlight passages and keep notes.
- Workbooks: working with the data3 minA working copy of your data for sorting, filtering, calculating and charting. The verified dataset is never changed.
- Writer: manuscripts and citations3 minWrite a manuscript in your project, cite papers from its library, and export a file anyone can open.
Assistance
The assistant: what it answers from, what it can do, and what it always asks you first.
Team and access
Roles, what each one can do, and how people are invited to a project.
Reference
The export fields, the property groups, the glossary, and how to suggest a change.
- Data dictionary2 minEvery field in the FoodProt AI export, listed in the order it is written.
- Suggesting a change1 minHow to suggest a change to the vocabulary, to your study rules or to the platform, and what makes a suggestion easy to act on.
- The 14 functionality groups4 minThe top-level groups every measured property belongs to, with the unit rules of each.
- The property glossary2 minWhere to find the definition, other names, accepted units and comparison rules for each of the 81 properties, and how to read an entry.
Running the platform
Troubleshooting, system status, account settings, and privacy.
- Troubleshooting2 minCommon problems, what each one means, and the first thing to check.
- System status1 minWhere to find System status, what it reports, and what to do when background work has stalled.
- Account creation settings1 minWho can sign up, how new accounts are protected, and how platform staff roles are appointed.
- Privacy and security2 minWhat is stored, who can read it, what is sent outside the platform, and what the platform never holds.
See also how the workflow works and how access works.