Missing disease information and evidence for "post-COVID-19 disorder"

[dhimmel]

As of OpenTargets 24.06 there is a disease page for MONDO:0100320 / "post-COVID-19 disorder" at https://platform.opentargets.org/disease/MONDO_0100320, but there is no evidence of any sort for this disease. The only disease information is that from the EFO OTAR Slim ontology:

Any insights into why this disease term receives no evidence or information besides its presence in EFO? Is it that no evidence maps to the EFO term or that the evidence is somehow getting filtered?

[ireneisdoomed]

This term was created a few months ago, so we might have evidence of post COVID that is not mapped. @vivienho, could you please do some checks?

• Are there any traits in the latest evidence that refer to post COVID? If so, it'd be nice to know the breakdown per source and how many of them have a mapped ID. Path would be gs://open-targets-pre-data-releases/24.09/input/evidence-files/
• Any target safety events that we could associate with post COVID? Path'd be gs://open-targets-pre-data-releases/24.09/input/target-inputs/safety/safetyLiabilities.json.gz
• Any diseases extracted from literature refer to post COVID? We can look at the datasets of both unmapped (gs://open-targets-pre-data-releases/24.06/output/etl/parquet/literature/failedMatches) and mapped (gs://open-targets-pre-data-releases/24.06/output/etl/parquet/literature/matches). These datasets contain all recognised entities, you want to filter by those of type == DS to get the list of diseases.

I would also normalise the traits by lowercasing them and removing any special characters.

If we find labels that are similar enough, we could ask EFO to list them as synonyms and ask our providers to update their mappings.

[vivienho]

@ireneisdoomed I had a look and only 2 evidence sources have traits that refer to post covid:

• ChemBL: 4 traits refer to post covid (2 mapped to id for covid, 2 not mapped)

  +-------------------------------------+-------------------------+
  |disease_lower                        |diseaseFromSourceMappedId|
  +-------------------------------------+-------------------------+
  |post-covid-19 syndrome               |MONDO_0100096            |
  |post acute sequelae covid-19 hyposmia|MONDO_0100096            |
  |post covid-19 anosmia (loss of smell)|NULL                     |
  |post-acute covid-19 syndrome         |NULL                     |
  +-------------------------------------+-------------------------+

• EVA: 1 trait refers to post covid (mapped to correct id but not showing up on platform)

  +----------------------+-------------------+-------------------------+
  |disease_lower         |diseaseFromSourceId|diseaseFromSourceMappedId|
  +----------------------+-------------------+-------------------------+
  |post-covid-19 disorder|CN305504           |MONDO_0100320            |
  +----------------------+-------------------+-------------------------+

No target safety events are associated with post covid

The matches dataset does not contain entities referring to post covid, but the failedMatches dataset contains 71 distinct entities referring to post covid:

+-------------------------------------------------------+
|label_lower                                            |
+-------------------------------------------------------+
|chronic post-covid-19 syndrome                         |
|mental post-covid syndrome                             |
|post-acute coronavirus (covid-19) syndrome             |
|post-covid-19 syndrome                                 |
|post-covid syndrome                                    |
|post-covid syndromes                                   |
|post-acute covid-19 syndrome                           |
|post-acute sequelae of covid-19                        |
|post covid-19                                          |
|post-covid-19 tachycardia syndrome                     |
|postcovid syndrome                                     |
|postcovidal syndrome                                   |
|post covid-19 syndrome                                 |
|post covid syndrome                                    |
|persistent post-covid syndrome                         |
|post-covid respiratory failure                         |
|post-covid-syndrome                                    |
|post-covid-19                                          |
|postcovid optic neuropathy                             |
|post-covid" syndrome                                   |
|postcovid diabetes                                     |
|post-covid-19 pneumonia                                |
|post-covid inflammatory syndrome                       |
|post-covid pulmonary fibrosis                          |
|post-acute coronavirus 2019 (covid-19) syndrome        |
|covid-19 postoperative infection                       |
|post acute coronavirus (covid-19) syndrome             |
|post-covid disorders syndrome                          |
|post‐covid‐19 syndrome                                 |
|post-covid' syndrome                                   |
|post-acute covid syndrome                              |
|post acute covid syndrome                              |
|postcovid disorders                                    |
|post‐covid syndrome                                    |
|postcovid syndromes                                    |
|post-covid guillan-barré syndrome                      |
|long post-covid vaccination syndrome                   |
|post-covid dysautonomia                                |
|post-covid-19 syndrome5                                |
|post-covid-19 nephropathies                            |
|post-acute coronavirus disease 2019 (covid-19) syndrome|
|post covid-19 neurological syndrome                    |
|post-acute covid-19                                    |
|post-covid neurological syndrome                       |
|post-acute coronavirus disease (covid) syndrome        |
|post-covid olfactory dysfunction                       |
|covid-19 postviral syndrome                            |
|post-covid                                             |
|post covid-ild                                         |
|post-coronavirus disease 2019 (covid-19) syndrome      |
|post-covid renal impairment                            |
|post-covid-19 cholangiopathy                           |
|post-covid neurologic syndrome                         |
|post acute covid-19 syndrome                           |
|post-covid" syndrome                                   |
|post-covid lung disease                                |
|postcovid asthenic syndrome                            |
|post-covid pneumonia syndrome                          |
|post-covid autonomic syndrome                          |
|post-coronavirus disease (covid) syndrome              |
|post-covid-19-syndrome                                 |
|post-covid organizing pneumonia                        |
|post-covid diseases                                    |
|post-covid disorder                                    |
|postcovid asthenia                                     |
|post-covid-syndroms                                    |
|post-covid syndrome5                                   |
|post-covid19 syndrome                                  |
|post-covid cholangiopathy                              |
|chronic post-covid syndrome                            |
|postacute covid syndrome                               |
+-------------------------------------------------------+