update convention link and array-valued metadata format info - #2
Conversation
| Examples: disease, species, organ | ||
|
|
||
| To allow query at varying levels of specificities, the Alexandria Metadata Convention uses ontology-valued metadata whenever possible. These ontologies are tree-structured heirarchies curated by experts and maintained by EBI. For the purposes of the Alexandria Metadata Convention, please select the most specific value in the heirarchy as possible. For use of this metadata during query of the Alexandria database, a query result will include all child values of the query term. Single Cell Portal treats these values as group, or categorical variables. | ||
| To allow query at varying levels of specificities, the Alexandria Metadata Convention uses ontology-valued metadata whenever possible. These ontologies are tree-structured hierarchies curated by experts and easily accessible through a [Lookup Service](https://www.ebi.ac.uk/ols/index) maintained by EBI. For the purposes of the Alexandria Metadata Convention, please select the most specific value in the hierarchy as possible. For use of this metadata during query of the Alexandria database, a query option can allow the inclusion of all child values of the query term. Single Cell Portal treats these values as group, or categorical variables. |
There was a problem hiding this comment.
Note "query option can allow the inclusion of all child values of the query term" is not yet an implemented feature for Alexandria. Can we decide on a phrasing to indicate that the functionality is on the roadmap but not yet available?
There was a problem hiding this comment.
"In a future update, querying this metadata on Alexandria will allow the inclusion of all its child values."? My understanding might be incomplete for this one.
Let me know whether you want to fix this before merging.
There was a problem hiding this comment.
Would it be acceptable to remove "For use of this metadata during query of the Alexandria database, a query option can allow the inclusion of all child values of the query term." and add something along this lines back to the documentation when the feature is available? It might be confusing to refer to functionality that has not yet been implemented.
| **Syntax in metadata file:** Array-valued metadata should be delimited using the pipe symbol (|): `[value1|value2|value3"]`. If the array-valued metadata only contains a single value, no special formatting is necessary. | ||
|
|
||
| If the array-valued metadata attribute is a dependant metadata attribute, the order in the array should correspond with the order of the array the attribute depends on. For example, the following metadata entries for `vaccination__ontology_label`: `"Influenza Virus Vaccine""BCG Vaccine"`, for `vaccination__time_since` : `"1","2"`, and for `vaccination__time_since__unit_label`: `"year","year"` would indicate that the Influenza vaccine was recieved 1 year ago and the BCG Vaccine was recieved 2 years ago. If information is not available for one of the metadata entries in a dependant array, include an empty string(`""`) for that value. | ||
| If the array-valued metadata attribute is a dependant metadata attribute, the order in the array should correspond with the order of the array the attribute depends on. For example, the following metadata entries for `vaccination__ontology_label`: `Influenza Virus Vaccine|BCG Vaccine`, for `vaccination__time_since` : `1|2`, and for `vaccination__time_since__unit_label`: `year|year` would indicate that the Influenza vaccine was recieved 1 year ago and the BCG Vaccine was recieved 2 years ago. If information is not available for one of the metadata entries in a dependant array, include a pipe symbol (`|`) at the appropriate location to indicate the lack of data. Example: `vaccination__time_since` : `|2`. |
There was a problem hiding this comment.
Had not thought about missing data in arrays so "If information is not available for one of the metadata entries in a dependant array, include a pipe symbol (|) at the appropriate location to indicate the lack of data" needs to be tested to see if it will work as currently described.
2 participants
There are a few items in the doc that we should discuss because the feature is either not yet implemented or needs to be tested. I'll put comments at the specific points in the doc to discuss in comments. This process can help us decide if future collaborative work on documentation is easier through Github or via Google docs.