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brynnz22 committed Aug 28, 2023
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#### ___Find___ Endpoints

The [find endpoints](https://api.microbiomedata.org/docs#/find:~:text=Find%20NMDC-,metadata,-entities.) are provided with NMDC metadata entites already specified - where metadata about [studies](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Study.html), [biosamples](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Biosample.html), [data objects](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/DataObject.html), and [activities](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Activity.html) can be retrieved using GET requests.
The [find endpoints](https://api.microbiomedata.org/docs#/find:~:text=Find%20NMDC-,metadata,-entities.) are provided with NMDC metadata entities already specified - where metadata about [studies](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Study.html), [biosamples](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Biosample.html), [data objects](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/DataObject.html), and [activities](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Activity.html) can be retrieved using GET requests.

The applicable parameters of the ___find___ endpoints, with acceptable syntax and examples, are in the table below.

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| group_by | Not yet implemented | Coming Soon | Not yet implemented |
| study_id | The unique identifier of a study | Curie e.g. `prefix:identifier` | `nmdc:sty-11-34xj1150` |
| sample_id | The unique identifier of a biosample | Curie e.g. `prefix:identifier` | `nmdc:bsm-11-w43vsm21` |
| data_object_id | The unique identifer of a data object | Curie e.g. `prefix:identifier` | `nmdc:dobj-11-7c6np651` |
| data_object_id | The unique identifier of a data object | Curie e.g. `prefix:identifier` | `nmdc:dobj-11-7c6np651` |
| activity_id | The unique identifier for an NMDC workflow execution activity | Curie e.g. `prefix:identifier` | `nmdc:wfmgan-11-hvcnga50.1`|<br/>
<br/>

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<br/>

![find get activities](../_static/images/howto_guides/api_gui/find_get_activities.png)
The `GET /activities` endpoint is a general way to fetch metadata about various activities (e.g. metagenome assembly, natural organic matter analysis, library preparation, etc.). Any "slot" (a.k.a. attribute) for [WorkflowExecutionActivty](https://microbiomedata.github.io/nmdc-schema/WorkflowExecutionActivity/) or [PlannedProcess](https://microbiomedata.github.io/nmdc-schema/PlannedProcess/) classes may be used in the filter and sort parameters, including attributes for subclasses of `WorkflowExecutionActvity` and `PlannedProcess`. For example, attributes used in subclasses such as, [MetabolomicsAnalysisActivity](https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/) (subclass of `WorkflowExecutionActivity`) or (Extraction)[https://microbiomedata.github.io/nmdc-schema/Extraction/] (subclass of `PlannedProcess`), can be used as input criteria for the filter and sort parameters of this endpoint.<br/>
The `GET /activities` endpoint is a general way to fetch metadata about various activities (e.g. metagenome assembly, natural organic matter analysis, library preparation, etc.). Any "slot" (a.k.a. attribute) for [WorkflowExecutionActivity](https://microbiomedata.github.io/nmdc-schema/WorkflowExecutionActivity/) or [PlannedProcess](https://microbiomedata.github.io/nmdc-schema/PlannedProcess/) classes may be used in the filter and sort parameters, including attributes for subclasses of `WorkflowExecutionActivity` and `PlannedProcess`. For example, attributes used in subclasses such as, [MetabolomicsAnalysisActivity](https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/) (subclass of `WorkflowExecutionActivity`) or (Extraction)[https://microbiomedata.github.io/nmdc-schema/Extraction/] (subclass of `PlannedProcess`), can be used as input criteria for the filter and sort parameters of this endpoint.<br/>
<br/>

![find get activities by activity id](../_static/images/howto_guides/api_gui/find_get_activities_activity_id.png)
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#### ___Metadata___ Endpoints

The [metadata endpoints](https://api.microbiomedata.org/docs#/metadata) can be used to get and filter metadata from collection set types (including studies, biosamples, activites, and data objects as discussed in the __find__ section).
The [metadata endpoints](https://api.microbiomedata.org/docs#/metadata) can be used to get and filter metadata from collection set types (including studies, biosamples, activities, and data objects as discussed in the __find__ section).

Unlike the compact syntax used in the __find__ endpoints, the syntax for the filter parameter of the metadata endpoints use [MongoDB-like language querying](https://www.mongodb.com/docs/manual/tutorial/query-documents/). The applicable parameters of the __metadata__ endpoints, with acceptable syntax and examples, are in the table below.

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| doc_id | The unique identifier of the item being requested. For example, the identifier of a biosample or an extraction | Curie e.g. `prefix:identifier` | `nmdc:bsm-11-ha3vfb58` |<br/>
<br/>

The __metadata__ endpoints allow users to retrieve metadata from the data portal using the various `GET` endpoints that are slightly different than the __find__ endpoints, but some can be used similarily. As with the __find__ endpoints, parameters for the __metadata__ endpoints that do not have a red `* required` next to them are optional. <br/>
The __metadata__ endpoints allow users to retrieve metadata from the data portal using the various `GET` endpoints that are slightly different than the __find__ endpoints, but some can be used similarly. As with the __find__ endpoints, parameters for the __metadata__ endpoints that do not have a red `* required` next to them are optional. <br/>
<br/>

![metadata get nmdcshema version](../_static/images/howto_guides/api_gui/metadata_get_nmdcschema_version.png)
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