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Update pyrice_instruction.rst
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docs/source/pyrice_instruction.rst

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@@ -226,8 +226,8 @@ Search new attributes on new databases
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Add new database
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^^^^^^^^^^^^^^^^^^^
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PyRice package supports queries on new databases by adding its description manually on `database_description.xml`.
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With JSON format, here is SNP-SEEK database with API: https://snp-seek.irri.org/ws/genomics/gene/osnippo/chr01?start=1&end=15000&model=iric::
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PyRice package supports queries on new databases by adding its description manually in `database_description.xml`.
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Using JSON format, here is an example with SNP-SEEK database API: https://snp-seek.irri.org/ws/genomics/gene/osnippo/chr01?start=1&end=15000&model=iric::
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<database dbname="snpseek" type="text/JSON" method="GET" normalize="false">
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<link stern="https://snp-seek.irri.org/ws/genomics/gene/osnippo/" aft=""/>
@@ -241,11 +241,11 @@ With JSON format, here is SNP-SEEK database with API: https://snp-seek.irri.org/
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For more details:
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- dbname : database name
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- type : the result return by API
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- method : GET/POST (usually GET)
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- normalize : normalize name of database true/false (usually false)
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- type : the result returned by API
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- method : GET/POST (default GET)
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- normalize : normalize name of database true/false (default false)
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- stern : URL of API
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- op : paramaters (see on API above)
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- op : parameters (see on API above)
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For example, with an API from Planteome: http://browser.planteome.org/api/search/annotation?bioentity=AT4G32150::
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@@ -288,4 +288,4 @@ To save the result, package uses the :py:func:`~pyrice.multi_query.MultiQuery.sa
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format=["csv", "html", "json", "pkl"], hyper_link=False)
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.. note:: With APIs return results with HTML and Javascript format, it might have some problems due to the difference of GUI (Javascript) or tag (HTML).
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So, we are working to simplize the package on those two formats to make it easier for updating new databases.
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So, we are working to simplize the package on those two formats to make it easier for updating new databases.

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