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User Manual -- winniGraph

1. Introduction

winniGraph is a web-based research platform for structured, project- and case-based research. Research work is organized in Workspaces. Within a Workspace, Research Cases, Notes, knowledge, structures, and research ideas can be developed and refined together.

A Research Case remains the central unit for a specific research task: you upload documents, ask targeted questions, and gradually build a persistent Research Memory or Knowledge Graph. When needed, winniGraph can also include external scientific sources.

This manual describes winniGraph from the user's perspective.

2. Core Concept: Workspace and Research Case

winniGraph distinguishes between two levels:

2.1 Workspace

A Workspace is the overarching working area for a research project. It combines different types of research information and provides several sections:

  • Overview -- overview of the Workspace
  • Cases -- Research Cases and specific research tasks
  • Notes -- private or shared notes
  • Knowledge -- consolidated Workspace knowledge
  • Structure -- structured organization of the research project
  • Ideas -- systematic discovery of new research directions

A Workspace can represent, for example, a master's thesis, dissertation, research project, or collaborative team project.

2.2 Research Case

A Research Case is a defined research task within a Workspace or research project. A Case can contain:

  • title and description
  • subject area
  • country context
  • uploaded documents
  • research questions
  • answers and result history
  • Case-specific Research Memory / Knowledge Graph

Use separate Cases for larger research questions that should remain clearly separated.

3. Registration, Plans, and Access

3.1 Registration and Login

You need an account with an email address and password. After signing in, you are taken to your dashboard.

3.2 Plans

The available functionality depends on your active plan. Typical variants include:

  • Individual -- personal research area
  • Team -- shared research area for up to 5 researchers plus 1 administrator

Without an active subscription, active research functionality may be restricted.

3.3 Teamwork

The Team plan supports collaborative research. Depending on permissions, shared content may include Workspaces, Cases, documents, results, Notes, and Research Memory. Research results retain information about which user initiated the research.

4. Dashboard and Workspaces

The dashboard is your central starting point. From there you can access your research areas and manage your plan.

A Workspace groups related research activities. When you open a Workspace, its navigation provides Overview, Cases, Notes, Knowledge, Structure, and Ideas.

Additional Workspace functions and settings are available in the Workspace header.

5. Overview

The Overview section provides a quick view of the current state of the Workspace.

It is intended to help you:

  • assess the scope and activity of the Workspace,
  • quickly understand what research content is available,
  • navigate between working areas,
  • review the current state of the research project.

Displayed statistics and summaries relate to the content currently stored in the Workspace.

6. Cases

6.1 Creating a New Case

Open Cases in the Workspace and select New Case or the corresponding create function.

When creating a Case, enter the required basic information. This may include:

  1. title
  2. optional description
  3. subject area
  4. additional contextual information

After saving, the Case can be used for document uploads and research questions.

6.2 Subject Areas

The subject area helps winniGraph adapt its research logic to the project. Depending on configuration, available areas may include:

  • Natural Sciences (Physics, Chemistry, Astronomy, Earth Sciences, Geology, Meteorology, Materials Science, Physical Chemistry)
  • Humanities (History, Philosophy, Linguistics, Literary Studies, Cultural Studies, Art History, Religious Studies, Archaeology, Media Studies)
  • Social Sciences (Sociology, Political Science, Economics, Psychology, Education, Communication Studies, Anthropology/Ethnology, Demography, Social Policy)
  • Medicine and Health (Medicine, Dentistry, Pharmacy, Nursing Science, Health Sciences/Public Health, Epidemiology, Clinical Research, Diagnostics, Therapy, Health Economics)
  • Life Sciences (Biology, Biochemistry, Molecular Biology, Genetics, Microbiology, Cell Biology, Neuroscience, Biotechnology, Bioinformatics, Ecology)
  • Environment/Climate (Environmental Sciences, Climate Research, Climatology, Sustainability Research, Environmental Ecology, Biodiversity, Conservation, Resource Management, Environmental Management, Renewable Energy, Environmental Policy)
  • Technology/Engineering (Mechanical Engineering, Electrical Engineering, Information Technology, Computer Science, Civil Engineering, Chemical/Process Engineering, Production Engineering, Mechatronics, Automation Engineering, Robotics, Energy Engineering, Transportation Engineering, Materials Engineering)
  • Formal Sciences (Mathematics, Statistics, Logic, Theoretical Computer Science, Data Science, Operations Research, Systems Science, Decision Theory, Mathematical Modelling)
  • Law (Legal Studies/Jurisprudence, Civil Law, Criminal Law, Public Law, Constitutional Law, Administrative Law, Labour Law, Social Law, Business Law, Tax Law, European Union Law, International Law, Data Protection Law, IT Law)

Choose the area that most closely matches your research question.

6.3 Country Context

A country can be selected for country-specific questions. This is particularly useful for legal, regulatory, economic, or application-related research.

Available countries may include EU member states, the United Kingdom, and the USA. Selecting a country does not generally exclude high-quality international scientific research.

7. Uploading Documents

Documents form the internal knowledge base of a Research Case.

7.1 Upload

  1. Open the relevant Case.
  2. Select a file in the upload section.
  3. Start the upload.
  4. Wait for processing to complete.

7.2 Processing

After upload, the file is assigned to the Case and analyzed in the background. Typical statuses are:

  • Idle -- processing has not started
  • Processing -- the document is being processed
  • Completed -- the document is available for research
  • Failed -- processing could not be completed

Whenever possible, wait until relevant documents have been fully processed before asking questions.

7.3 Limits

Upload quotas and maximum file sizes may depend on your plan. The application will indicate when a limit has been reached.

8. Asking Research Questions

Once documents have been processed, you can ask questions within a Case.

Good questions have a clear objective, identify a specific aspect, and include relevant constraints or context.

Examples:

  • "What are the main arguments in the uploaded documents in favor of this method?"
  • "What differences do the documents show between Germany and the USA?"
  • "Summarize the most important risks and opportunities identified in the sources."
  • "Which statements in my documents are well supported by scientific evidence?"

After submission, the research request is processed in the background. The result remains associated with the Case and can be reviewed later.

9. Results and Research Memory

Depending on the question, results may include:

  • direct answers
  • summaries and evaluations of internal documents
  • findings from Research Memory
  • relevant claims, entities, and relationships
  • document and source references
  • external scientific evidence when requested
  • structured information for further use

Multiple research requests within a Case form a history. Relevant findings can become part of the Case-specific Research Memory or Knowledge Graph and may be considered in later questions.

Internal documents and external evidence should remain distinguishable. Contradictions should remain visible rather than being silently merged into a single conclusion.

10. Notes

Notes are used to record thoughts, observations, intermediate findings, and other information directly in the Workspace.

10.1 Creating a Note

Open Notes and use New Note to create a new note.

10.2 Shared and Private

Notes have two visibility states:

  • Shared -- the Note can be used in the shared Workspace context.
  • Private -- the Note remains private.

When creating a Note, Shared is selected by default. When editing a Note, its visibility can be changed between Shared and Private.

10.3 Editing Notes

When an existing Note is opened, its saved visibility state is selected. A private Note can therefore later be shared, or a shared Note can be changed to private, provided it has not been locked because of subsequent use.

Notes that have already been used in certain group analyses may be protected from later modification.

10.4 Useful Applications

Notes are useful for:

  • hypotheses
  • open questions
  • methodological considerations
  • literature references
  • observations
  • intermediate findings
  • thoughts that may later contribute to research structure or further analysis

11. Knowledge

The Knowledge section provides access to knowledge accumulated within the Workspace.

While individual Cases contain specific research processes, Knowledge helps place findings in the broader context of the Workspace.

The goal is not merely to collect isolated answers, but to develop an increasingly consistent knowledge base in which relevant research information can be reused.

When interpreting this knowledge, continue to distinguish between your own documents, previous research results, and external evidence where applicable.

12. Structure

The Structure section supports the organized development of a research project.

It helps you view available content not merely as separate documents, Notes, or research results, but as parts of a broader research context.

Depending on the state of your project, Structure can help organize themes, research areas, and relationships more clearly.

Structure does not replace research itself. It builds on information already available in the Workspace and supports its organized reuse.

13. Ideas -- Discovering New Research Directions

The Ideas section supports systematic development of new research questions and research directions from existing material.

13.1 Starting Point

Idea Discovery uses selected source material as its primary starting point. Existing Workspace context can also be taken into account.

The system analyzes the source material, compares it with existing Workspace knowledge, identifies gaps, and develops possible new research directions.

13.2 Additional Scope

Under Additional scope (optional) you can add further context to Idea Discovery.

There are two independent options:

  • select additional Cases as context
  • enable Also check external research

Both are checkbox options and can be used at the same time.

Additional Cases do not replace the primary source document. They extend the context available to the analysis.

13.3 Selecting Multiple Cases

If several suitable Cases are available, multiple Cases can be selected simultaneously. This allows Idea Discovery to consider relationships across research areas that have already been explored.

13.4 External Research Check

Enable Also check external research to check whether external research already exists for a detected topic or potential research gap.

This check is optional and independent of additional Case selection.

13.5 Starting Idea Discovery

After selecting the source material and any additional scope, start the process with Discover research directions.

Processing takes place in the background. The system may perform several stages:

  1. analyze source material
  2. retrieve prioritized internal information
  3. compare it with existing Workspace knowledge
  4. optionally check existing external research
  5. assess knowledge or research gaps
  6. generate possible research ideas or directions

Generated ideas should be treated as starting points for further scientific assessment, not as substitutes for expert evaluation by the researcher.

14. External Scientific Research

External research is not automatically performed for every standard Case question. winniGraph primarily uses internal documents and existing Research Memory.

External research can be requested specifically to:

  • find recent studies,
  • compare internal findings with external literature,
  • identify supporting or contradicting evidence,
  • investigate potential research gaps,
  • consider the current state of research.

Preference is given to scientifically reliable sources such as peer-reviewed articles, original studies, reviews, meta-analyses, scientific repositories, universities, research institutes, and official institutions.

In Ideas, an external check can be explicitly enabled with Also check external research.

15. Collaboration in a Workspace

Workspaces support project-based collaboration.

A key principle is the deliberate distinction between shared and private information. Notes in particular can be marked Shared or Private.

Research Cases and their results can be used collaboratively depending on the plan and permissions. Over time, a Workspace can therefore develop into a shared research and knowledge environment.

For larger research projects, the following workflow is recommended:

  1. create or open a Workspace for the research project
  2. define the topic and objective clearly
  3. create suitable Cases for specific research questions
  4. upload relevant documents
  5. wait for document processing
  6. ask targeted questions within the Cases
  7. record important thoughts and intermediate findings as Notes
  8. deliberately choose Shared or Private
  9. review accumulated Knowledge and project Structure regularly
  10. use Ideas to investigate new research directions or potential gaps
  11. include additional Cases in Idea Discovery when useful
  12. add external research where it is relevant to the question

17. Tips for Better Results

Keep Cases Clearly Separated

Use separate Cases for clearly different research questions. This improves traceability and prevents unnecessary mixing of context.

Use High-Quality Sources

The quality of internal documents affects research quality. Prefer relevant and reliable material.

Ask Precise Questions

Specific questions generally produce more useful results than broad combined questions.

Use Notes Deliberately

Use Notes for thoughts and intermediate findings that do not require a new research request.

Choose Shared and Private Deliberately

Only share Notes that genuinely belong in the collaborative research context.

Do Not Treat Ideas as Final Research Findings

Idea Discovery identifies possible research directions and gaps. Generated suggestions require expert assessment and, where appropriate, validation through literature and further research.

Use External Research Selectively

External checking is particularly useful when novelty, current evidence, or a potential research gap needs to be assessed.

18. Common Problems and Solutions

A Document Remains in Processing

Refresh the page and check its status. Processing may still be running or may have failed.

Research Results Are Not Useful

Check whether document processing is complete, whether the question is sufficiently precise, and whether suitable sources are available in the Case.

A Shared Case or Content Is Not Visible

Check your team membership and permissions.

A Note Can No Longer Be Edited

A Note already used in certain analyses may be protected from later modification.

Ideas Has Too Little Context

Open Additional scope (optional) and select one or more additional Cases where useful.

I Want to Use Cases and External Research at the Same Time

You can. Case selection and Also check external research are independent checkboxes and can be enabled simultaneously.

External Research Is Not Being Performed

For standard Case research, external research is not necessarily started automatically. Explicitly request external evidence. In Idea Discovery, use Also check external research.

19. Deleting Data and Making Changes Carefully

Delete Cases only when their documents and results are no longer required. Related research information may be lost.

For shared content, also consider whether information has already been used in further analyses or collaborative workflows before changing it.

20. Managing Your Subscription

Depending on your plan model, the dashboard or billing portal can be used to:

  • check plan status,
  • manage payment details,
  • change plans,
  • manage an existing subscription.

21. Quick Start Guide

New Research Project

  1. sign in
  2. create or open a Workspace
  3. create a Research Case
  4. upload documents
  5. wait for processing
  6. ask research questions
  7. review results
  8. record relevant thoughts as Notes
  9. develop Knowledge and Structure
  10. use Ideas to explore new research directions

Idea Discovery

  1. open Ideas
  2. select the source material
  3. open Additional scope if needed
  4. select additional Cases
  5. optionally enable Also check external research
  6. use both options simultaneously when appropriate
  7. select Discover research directions
  8. assess the generated research directions critically

22. Summary

winniGraph combines specific Research Cases with an overarching Workspace. This allows individual research processes, documents, and results to be used as parts of a growing research project rather than only in isolation.

The Workspace sections serve different purposes:

  • Overview -- project overview
  • Cases -- specific research
  • Notes -- thoughts and intermediate findings
  • Knowledge -- accumulated knowledge
  • Structure -- organization of the research project
  • Ideas -- development of new research directions

A well-structured Workspace, high-quality documents, precise questions, and deliberate use of internal and external evidence provide the foundation for transparent and consistent research with winniGraph.