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update empo (#3194)
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‎qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst‎

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@@ -77,41 +77,57 @@ Remember, metadata is the most important part for an analysis, without it we onl
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7. *elevation*, *latitude*, *longitude*
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8. *physical_specimen_location*
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9. *collection_timestamp*
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10. *empo_1*, *empo_2*, *empo_3*
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10. *empo_1*, *empo_2*, *empo_3*, *empo_4*, more info: :ref:`empo`
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.. table::
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:widths: auto
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=============== ================= ======================= ================================================================================
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empo_1 empo_2 empo_3 Examples
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Free-living Non-saline Water (non-saline) fresh water from lake, pond, or river (<5 psu)
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Free-living Non-saline Sediment (non-saline) sediment from lake, pond, or river (<5 psu)
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Free-living Non-saline Soil (non-saline) soil from forest, grassland, tundra, desert, etc.
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Free-living Non-saline Surface (non-saline) biofilm from wet (<5 psu) or dry surface, wood, dust, or microbial mat
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Free-living Non-saline Subsurface (non-saline) deep or subsurface environment
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Free-living Non-saline Aerosol (non-saline) aerosolized dust or liquid
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Free-living Saline Water (saline) salt water from ocean, sea, estuary, mangrove, or coral reef (>5 psu)
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Free-living Saline Sediment (saline) sediment from ocean, sea, estuary, mangrove, or beach (>5 psu)
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Free-living Saline Hypersaline (saline) water from hypersaline sample or brine (>50 psu)
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Free-living Saline Surface (saline) biofilm from wet or underwater surface or microbial mat (>5 psu)
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Free-living Saline Aerosol (saline) seaspray or other aerosolized saline material (>5 psu)
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Host-associated Animal-associated Animal distal gut feces, stool
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Host-associated Animal-associated Animal proximal gut digesta
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Host-associated Animal-associated Animal secretion gut intestine, gizzard, crop, lumen, or mucosa
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Host-associated Animal-associated Animal surface skin, sebum, mucus, slime
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Host-associated Animal-associated Animal corpus tissue of sponge, coral, gill, siphon, carcass, etc. or whole small animal
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Host-associated Fungus-associated Fungus corpus tissue of mushroom or other fungi
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Host-associated Fungus-associated Fungus surface biofilm of mushroom
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Host-associated Plant-associated Plant secretion pollen or sap
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Host-associated Plant-associated Plant surface leaf or kelp surface biofilm
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Host-associated Plant-associated Plant rhizosphere plant root system, may include some soil
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Host-associated Plant-associated Plant corpus tissue of leaf, stem, fruit, or algae
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Control Negative Sterile water blank sterile water blank used as negative control for extraction, PCR, and sequencing
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Control Positive Mock community known mixed community used as positive control
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Control Positive Single strain known single strain control culture
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Unknown Contradictory Unknown (contradictory) unknown sample type because other metadata is contradictory
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Unknown Missing Unknown (missing) unknown sample type because metadata is unavailable
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=============== ================= ======================= ================================================================================
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================ ============================ ==================== ================================ =======================================================================================================================================
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empo_1 empo_2 empo_3 empo_4 Examples
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Control Negative Sterile water blank Sterile water blank sterile water blank used as negative control for extraction, PCR, and sequencing
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Control Positive Mock community Mock community known mixed community used as positive control
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Control Positive Single strain Single strain known single strain used as positive control
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Free-living Free-living (non-saline) Aqueous (non-saline) Aerosol (non-saline) aerosolized dust or liquid
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Free-living Free-living (non-saline) Aqueous (non-saline) Surface (non-saline) biofilm from wet (<5 psu) or dry surface, wood, dust, microbial mat
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Free-living Free-living (non-saline) Aqueous (non-saline) Water (non-saline) fresh water from lake, pond, river (<5 psu)
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Free-living Free-living (non-saline) Solid (non-saline) Sediment (non-saline) sediment from lake, pond, river (<5 psu)
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Free-living Free-living (non-saline) Solid (non-saline) Soil (non-saline) soil from forest, grassland, tundra, desert, etc.
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Free-living Free-living (non-saline) Solid (non-saline) Subsurface (non-saline) deep or subsurface environment
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Free-living Free-living (non-saline) Solid (non-saline) Surface (non-saline) dust or biofilm from dry surface such as floors, keyboards, door handles, and filters
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Free-living Free-living (saline) Aqueous (saline) Aerosol (saline) seaspray or other aerosolized saline material (>5 psu)
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Free-living Free-living (saline) Aqueous (saline) Hypersaline (saline) water from hypersaline sample or brine (>50 psu)-
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Free-living Free-living (saline) Aqueous (saline) Surface (saline) biofilm from wet or underwater surface or microbial mat (>5 psu)
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Free-living Free-living (saline) Aqueous (saline) Water (saline) salt water from ocean, sea, estuary, mangrove, coral reef (>5 psu)
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Free-living Free-living (saline) Solid (saline) Sediment (saline) sediment from ocean, sea, estuary, mangrove, beach (>5 psu)
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Free-living Free-living (saline) Solid (saline) Soil (saline) saline or hypersaline soil from forest, grassland, tundra, desert, etc.
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Free-living Free-living (saline) Solid (saline) Subsurface (saline) deep or subsurface saline environment
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Host-associated Host-associated (non-saline) Animal (non-saline) Animal corpus (non-saline) tissue, carcass, etc., or whole small terrestrial or freshwater animal
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Host-associated Host-associated (non-saline) Animal (non-saline) Animal distal gut (non-saline) feces, stool from terrestrial or freshwater animal
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Host-associated Host-associated (non-saline) Animal (non-saline) Animal proximal gut (non-saline) gut intestine, gizzard, crop, lumen, mucosa from terrestrial or freshwater animal
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Host-associated Host-associated (non-saline) Animal (non-saline) Animal secretion (non-saline) saliva, breast milk, vaginal secretion from terrestrial or freshwater animal
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Host-associated Host-associated (non-saline) Animal (non-saline) Animal surface (non-saline) skin, sebum, mucus, slime from terrestrial or freshwater animal
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Host-associated Host-associated (non-saline) Fungus (non-saline) Fungus corpus (non-saline) tissue of fruiting body or thallus or other fungal structure; terrestrial or freshwater
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Host-associated Host-associated (non-saline) Fungus (non-saline) Fungus surface (non-saline) biofilm of fruiting body or thallus or other fungal structure; terrestrial or freshwater
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Host-associated Host-associated (non-saline) Plant (non-saline) Plant detritus (non-saline) root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal interior/tissue; terrestrial or freshwater
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Host-associated Host-associated (non-saline) Plant (non-saline) Plant rhizosphere (non-saline) plant root system, may include some soil; terrestrial or freshwater
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Host-associated Host-associated (non-saline) Plant (non-saline) Plant secretion (non-saline) pollen, sap; terrestrial or freshwater
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Host-associated Host-associated (non-saline) Plant (non-saline) Plant surface (non-saline) root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal surface biofilm; terrestrial or freshwater
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Host-associated Host-associated (saline) Animal (saline) Animal corpus (saline) tissue of sponge, coral, gill, siphon, carcass, etc. or whole small marine animal
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Host-associated Host-associated (saline) Animal (saline) Animal distal gut (saline) feces, stool from marine animal
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Host-associated Host-associated (saline) Animal (saline) Animal proximal gut (saline) gut intestine, gizzard, crop, lumen, mucosa from marine animal
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Host-associated Host-associated (saline) Animal (saline) Animal secretion (saline) saliva, breast milk, vaginal secretion from marine animal
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Host-associated Host-associated (saline) Animal (saline) Animal surface (saline) skin, sebum, mucus, slime from marine animal
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Host-associated Host-associated (saline) Fungus (saline) Fungus corpus (saline) tissue of fruiting body or thallus or other fungal structure; marine
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Host-associated Host-associated (saline) Fungus (saline) Fungus surface (saline) biofilm of fruiting body or thallus or other fungal structure; marine
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Host-associated Host-associated (saline) Plant (saline) Plant detritus (saline) root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal interior/tissue; marine
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Host-associated Host-associated (saline) Plant (saline) Plant rhizosphere (saline) plant root system, may include some soil; marine
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Host-associated Host-associated (saline) Plant (saline) Plant secretion (saline) pollen, sap; marine
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Host-associated Host-associated (saline) Plant (saline) Plant surface (saline) root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal surface biofilm; marine
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not applicable not applicable not applicable not applicable information is inappropriate to report, can indicate that the standard itself fails to model or represent the information appropriately
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missing not collected not collected not collected information of an expected format was not given because it has not been collected
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missing not provided not provided not provided information of an expected format was not given, a value may be given at a later stage
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missing restricted access restricted access restricted access information exists but can not be released openly because of privacy concerns
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================ ============================ ==================== ================================ =======================================================================================================================================
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c. Extra minimal information for host associated studies:
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‎qiita_pet/support_files/doc/source/empo.rst‎

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.. _empo:
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Earth Microbiome Project Ontology (EMPO)
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========================================
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Qiita supports using the EMPO classification of samples as it provides and easy
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way to group samples and has resulted extremely helpful for meta-analyses and
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searching and finding similar samples in the database.
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The current version can be found here: :ref:`checklist-for-ebi-ena-submission` and below
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you can find older version, for your reference.
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EMPO 1 (first release)
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----------------------
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.. table::
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:widths: auto
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=============== ================= ======================= ================================================================================
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empo_1 empo_2 empo_3 Examples
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Free-living Non-saline Water (non-saline) fresh water from lake, pond, or river (<5 psu)
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Free-living Non-saline Sediment (non-saline) sediment from lake, pond, or river (<5 psu)
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Free-living Non-saline Soil (non-saline) soil from forest, grassland, tundra, desert, etc.
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Free-living Non-saline Surface (non-saline) biofilm from wet (<5 psu) or dry surface, wood, dust, or microbial mat
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Free-living Non-saline Subsurface (non-saline) deep or subsurface environment
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Free-living Non-saline Aerosol (non-saline) aerosolized dust or liquid
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Free-living Saline Water (saline) salt water from ocean, sea, estuary, mangrove, or coral reef (>5 psu)
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Free-living Saline Sediment (saline) sediment from ocean, sea, estuary, mangrove, or beach (>5 psu)
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Free-living Saline Hypersaline (saline) water from hypersaline sample or brine (>50 psu)
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Free-living Saline Surface (saline) biofilm from wet or underwater surface or microbial mat (>5 psu)
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Free-living Saline Aerosol (saline) seaspray or other aerosolized saline material (>5 psu)
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Host-associated Animal-associated Animal distal gut feces, stool
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Host-associated Animal-associated Animal proximal gut digesta
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Host-associated Animal-associated Animal secretion gut intestine, gizzard, crop, lumen, or mucosa
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Host-associated Animal-associated Animal surface skin, sebum, mucus, slime
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Host-associated Animal-associated Animal corpus tissue of sponge, coral, gill, siphon, carcass, etc. or whole small animal
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Host-associated Fungus-associated Fungus corpus tissue of mushroom or other fungi
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Host-associated Fungus-associated Fungus surface biofilm of mushroom
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Host-associated Plant-associated Plant secretion pollen or sap
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Host-associated Plant-associated Plant surface leaf or kelp surface biofilm
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Host-associated Plant-associated Plant rhizosphere plant root system, may include some soil
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Host-associated Plant-associated Plant corpus tissue of leaf, stem, fruit, or algae
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Control Negative Sterile water blank sterile water blank used as negative control for extraction, PCR, and sequencing
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Control Positive Mock community known mixed community used as positive control
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Control Positive Single strain known single strain control culture
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Unknown Contradictory Unknown (contradictory) unknown sample type because other metadata is contradictory
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Unknown Missing Unknown (missing) unknown sample type because metadata is unavailable
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=============== ================= ======================= ================================================================================

‎qiita_pet/support_files/doc/source/index.rst‎

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.. toctree::
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checklist-for-ebi-ena-submission
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empo
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Looking for comparable studies? Please see the document here:
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