Skip to the content.

Knowledge curation management

Please keep your progress frequently and save or update your files after completing a knowledge mining of a literature, which may save you from losing your current work progress.

Share your results

Visit OpenProphetDB for the current ongoing projects and contact the appropriate project group members to invite them to join the appropriate Organization.


There will be a meeting every two weeks to track the literature knowledge mining progress and discuss related issues, and you can watch it through the link below,

Meeting link: Ask the administrator for the link.

Video link of the previous conference: Ask the administrator for the link.

Improve your labeling situation

On the annotation page, you can see the top tab to see the team members or add your annotation.

Meanwhile, please improve your annotation status as follows:

Preliminary consideration


Color schemes

At present, there is no standard color scheme, and each label and color scheme can be modified and improved according to the requirements.

The existing labels and color matching are considered to set the principle of easy to distinguish and not easy to confuse. After the color, the characters (numbers or letters) are shortcut keys, which can be quickly selected and marked by the corresponding characters on the keyboard.

ID identifiers

To implement an automatic annotation of the biochemical entities, consider:


Common questions

Q1: Proteins cannot be aligned in the Knowledge Graph Editor, such as interleukin-8 / IL-8.

A1: IL-8 is interleukin-8, a cytokine produced by a variety of cells and is a protein entity. Since proteins align to gene entities in the Knowledge Graph Editor, a search in NCBI yields that the gene ID of IL-8 is CXCL8, and searching for CXCL8 in the editor will bring up the corresponding entity and complete the editing.

Q2: Different names for the same entity, such as Post-Acute Sequelae of SARS-CoV-2 infection (PASC) or Long-haul COVID or Post-COVID-19 Syndrome or Post-Acute COVID-19 Syndrome

A2: Unified alignment is Long COVID-19 MONDO:0100233.

Q3: Can I find entities by their IDs when aligning in the Knowledge Graph Editor?

A3: Of course you can! If you enter MONDO:0100233, the entity Long COVID-19 will be searched.

Q4: How should I mark a ratio or multiple side-by-side entities in the markup content?

A4: Mark each entity and indicate the ratio by key phrases in the alignment editor.

Q5: In which label do immune cells such as B cells, T cells, human lung cells, and cardiomyocytes count?

A5: Immune cells can be labeled as B/T cell activation under Biological Processes, and lung cells and cardiomyocytes can be labeled as Lung and Heart under Anatomical Structures.

Q6: What will it look like if I have labeled some entities on Label Studio, but don’t go further to Knowledge Graph-Editor to modify the entity?

A6: Then it is not possible to import the data into and form the Knowledge Graph, so this step must be needed!

Q7: Why I have no way to use the latest version?

A7: It is recommended to clear the browser cache or use the no-trace browsing mode, Google Chrome is recommended.

Q8: Why can’t I search for a certain entity?

A8: First of all, check the editor to input less than 3 letters, in order to improve the accuracy of the search, the search less than 3 letters will not be displayed; secondly, the entity is not normalized, it is recommended to use the normalized entity name; lastly, the entity does not exist in the database, please mark it as Unknown.

Q9: When 2 entities appear in the same article, they must have some kind of connection, so associate with is used in what situation?

A9: There are two cases. On one hand, for both entities, when their relationship is clearly mentioned in the article, but there is no option in the list, you can feed back to the developer to add the relationship. On the other hand, be associated with can be used when the author is also not clear about the relationship.

Q10: What is difference between Downregulated in, Reduced by, Alleviated by?

A10: Downregulated in: a reduction in the level of gene expression or a biological process, Reduced by: a quantitative or numerical reduction, Alleviated by: a reduction in the level of gene expression or a biological process -focused on disease alleviating symptoms or discomfort.