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Merge branch 'update_ext_res' of https://github.com/NeurodataWithoutBorders/nwb-overview into update_ext_res
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docs/source/external_resources_entity_guide.rst

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@@ -16,10 +16,10 @@ external **ontology**, **registry**, or **atlas**; for example linking the speci
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machine-readable, and interoperable, enabling tools to group, search, and compare data across
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files and labs because everyone points at the same canonical identifier.
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In NWB, these links are stored using **HERD** (HDMF External Resources Data Structure). HERD is a
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dedicated data structure for attaching external references to existing values in a file.
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HERD stores for each annotation, the term as it appears in your file, the location where it is used,
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along with a compact identifier (``entity_id``) and a resolvable URL (``entity_uri``) for the
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In NWB, these links are stored using **HERD** (HDMF External Resources Data Structure). HERD is a
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dedicated data structure for attaching external references to existing values in a file.
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HERD stores, for each annotation, the term as it appears in your file and the location where it is used,
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along with a compact identifier (``entity_id``) and a resolvable URL (``entity_uri``) for the
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external entry.
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To simplify the use of external resources, **TermSets** defined via LinkML can be used to
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How to add external resources to an NWB file
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--------------------------------------------
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**PyNWB tutorials**: The following tutorials provide a practical guide to using HERD and TermSet in PyNWB:
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**PyNWB tutorials**: The following tutorials provide a practical guide to using HERD and TermSets in PyNWB:
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* :pynwb-docs:`Linking to External Resources <tutorials/general/plot_external_resources.html>`:
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Learn how to use HERD to annotate a single NWB file with external resources in PyNWB.
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* :pynwb-docs:`Annotating Multiple Files <https://pynwb.readthedocs.io/en/stable/tutorials/general/resources_streaming.html>`:
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* :pynwb-docs:`Annotating Multiple Files <tutorials/general/resources_streaming.html>`:
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Learn how to use HERD to annotate multiple remote NWB files using streaming to avoid downloading them all.
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* :pynwb-docs:`TermSet for Validation <tutorials/general/plot_configurator.html>`: Learn how to configure PyNWB
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to automatically use pre-configured TermSets to validate terms and automatically populate HERD.

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