From 522c2cb8950062020ad14ab9395c36a2cbae568f Mon Sep 17 00:00:00 2001 From: Peter Woollard <115020636+Woolly-at-EBI@users.noreply.github.com> Date: Fri, 10 Nov 2023 15:44:24 +0000 Subject: [PATCH] Update tag_querying.rst Reformatted all the tables to force wrapping, as Sphinx can't handle this welll. Rather laborious. Used ChaptGTP do much of the formatting, but still needed to fine tune it. --- .../programmatic-access/tag_querying.rst | 355 ++++++++---------- 1 file changed, 167 insertions(+), 188 deletions(-) diff --git a/retrieval/programmatic-access/tag_querying.rst b/retrieval/programmatic-access/tag_querying.rst index 148bd3d..181aac6 100644 --- a/retrieval/programmatic-access/tag_querying.rst +++ b/retrieval/programmatic-access/tag_querying.rst @@ -47,198 +47,177 @@ Most of the sample and taxonomy tags have the format: high_level_tag:low_level_ Table of Object High Level Tags ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. csv-table:: High Level Tags - :header: "high level tag", "description", "object type" - :widths: 20, 300, 50 - - "pathogen", "The sample has been automatically determined to belong to the Pathogens Portal", "assembly; sample; sequence; study; secondary_study; taxonomy" - "coastal_brackish", "The sample has been automatically determined by evaluation of GPS and other parameters to have some evidence of being collected from either a coastal or brackish environment.", "read_run; sample; taxonomy" - "freshwater", "The sample has been automatically determined by evaluation of GPS and other parameters to have some evidence of being collected from a freshwater environment.", "read_run; sample; taxonomy" - "marine", "The sample has been automatically determined by evaluation of GPS and other parameters to have some evidence of being collected from a marine environment.", "read_run; sample; taxonomy" - "terrestrial", "The sample has been automatically determined by evaluation of GPS and other parameters to have some evidence of being collected from a terrestrial environment.", "read_run; sample; taxonomy" - "datahub", "The sample has been automatically determined to belong to a datahub. Currently tags have been generated for `FAANG `_ and `Pathogen `_", "analysis; read_run; sample; secondary_study" - "xref", "The sample has been referenced in an external to the EMBL-EBI repository. Currently tags have been generated for WORMS and UniEUK.", "Depends on how the user submitted" - "covid19", "The sample has been automatically determined to belong to the COVID19 portal.", "analysis; read_run; sample; sequence; study" - - - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Table of All Object High and Low Level Tags -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +| high level tag | description | object type | ++===================+=========================================================+======================================================+ +|| pathogen || The sample has been automatically determined to || assembly; sample; sequence; study; secondary_study; | +|| || belong to the Pathogens Portal || taxonomy | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| coastal_brackish || The sample has been automatically determined to || read_run; sample; taxonomy | +|| || evaluation of GPS and other parameters to have || | +|| || some evidence of being collected from either a || | +|| || coastal or brackish environment || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| freshwater || The sample has been automatically determined to || read_run; sample; taxonomy | +|| || evaluation of GPS and other parameters to have || | +|| || some evidence of being collected from a || | +|| || freshwater environment || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| marine || The sample has been automatically determined to || read_run; sample; taxonomy | +|| || evaluation of GPS and other parameters to have || | +|| || some evidence of being collected from a || | +|| || marine environment || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| terrestrial || The sample has been automatically determined to || read_run; sample; taxonomy | +|| || evaluation of GPS and other parameters to have || | +|| || some evidence of being collected from a || | +|| || terrestrial environment || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| datahub || The sample has been referenced to a datahub || analysis; read_run; sample; secondary_study | +|| || Currently tags have been generated for || | +|| || `FAANG ` and || | +|| || `Pathogen ` || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| xrefs || The sample has been referenced to am external || Depends on how the user submitted | +|| || to the EMBL-EBI repository. Currently tags have || | +|| || been generated for WORMS and UniEUK || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ +|| covid19 || The sample has been automatically determined to || analysis; read_run; sample; sequence; study | +|| || belong to the COVID19 portal || | ++-------------------+---------------------------------------------------------+------------------------------------------------------+ + + + + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Tables of All Object High and Low Level Tags +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ These are at several types of objects especially sample and taxonomy. Please see the object types in the previous (high level tag) table, to see what they apply to. -.. list-table:: Object High and Low Level Tags - :widths: 15 10 30 10 10 - :header-rows: 1 - - * - tag presentation - - high level tag - - low level tag - - description - - comment - * - pathogen - - pathogen - - - - Object is some type of pathogen - - There will likely be other low level tags to provide context. - * - pathogen:priority - - pathogen - - priority - - - - - * - pathogen:bacterium - - pathogen - - bacterium - - Object is of a bacterium organism. - - At time of documentation the bacterium is not specifically pathogenic. - * - pathogen:fungus - - pathogen - - fungus - - Object is of a fungus orgnism. - - At time of documentation the fungus is not specifically pathogenic. - * - pathogen:helminth - - pathogen - - helminth - - - - At time of documentation the helminth is not specifically pathogenic. - * - pathogen:protozoan - - pathogen - - protozoan - - Object is of a protozon organism. - - At time of documentation the protozoan is not specifically pathogenic. - * - pathogen:virus - - pathogen - - virus - - Object is of a virus organism. - - At time of documentation the virus is not specifically pathogenic. - * - coastal_brackish - - coastal_brackish - - - - Some evidence that the object is “coastal or brackish” environment associated. - - There will likely be other low level tags to provide context. - * - coastal_brackish:high_confidence - - coastal_brackish - - high_confidence - - strong evidence that the object is “coastal or brackish” environment associated. - - - * - coastal_brackish:medium_confidence - - coastal_brackish - - medium_confidence - - moderate evidence that the object is “coastal or brackish” environment associated. - - - * - coastal_brackish:low_confidence - - coastal_brackish - - low_confidence - - weak evidence that the object is “coastal or brackish” environment associated. - - - * - freshwater - - freshwater - - - - Some evidence that it is “freshwater” environment assosciated - - There will likely be other low level tags to provide context. - * - freshwater:high_confidence - - freshwater - - high_confidence - - Strong evidence that the object is freshwater environment associated. - - - * - freshwater:medium_confidence - - freshwater - - medium_confidence - - moderate evidence that the object is freshwater environment associated. - - - * - freshwater:low_confidence - - freshwater - - low_confidence - - weak evidence that the object is freshwater environment associated. - - - * - marine - - marine - - - - Some evidence that it is “marine” environment assosciated - - There will likely be other low level tags to provide context. - * - marine:high_confidence - - marine - - high_confidence - - Strong evidence that the object is marine environment associated. - - - * - marine:medium_confidence - - marine - - medium_confidence - - moderate evidence that the object is marine environment associated. - - - * - marine:low_confidence - - marine - - low_confidence - - weak evidence that the object is marine environment associated. - - - * - terrestrial - - terrestrial - - - - Some evidence that it is terrestrial(land) environment associated. - - There will likely be other low level tags to provide context. - * - terrestrial:high_confidence - - terrestrial - - high_confidence - - Strong evidence that the object is terrestrial(land) environment associated. - - - * - terrestrial:medium_confidence - - terrestrial - - medium_confidence - - moderate evidence that the object is terrestrial(land) environment associated. - - - * - terrestrial:low_confidence - - terrestrial - - low_confidence - - weak evidence that the object is terrestrial(land) environment associated. - - - * - datahub:faang - - datahub - - Faang - - Is a `Functional Annotation of ANimal Genomes project (FAANG) `_ sample and present in that datahub - - - * - datahub:metagenome - - datahub - - metagenome - - Is a metagenome and present in that datahub - - - * - xref:arrayexpress - - xref - - arrayexpress - - Object associated with an `ArrayExpress `_ record - - A xref is available that links to ArrayExpress - * - xref:europepmc - - xref - - europepmc - - Object associated with a `European PubmedCentral `_ record - - A xref is available that links to European PubmedCentral - * - xref:pubmed - - xref - - pubmed - - Object associated with an `NCBI Pubmed `_ record - - A xref is available that links to NCBI Pubmed - * - xref:worms - - xref - - worms - - Object associated with a `WoRMS `_ record - - - * - xref:unieuk - - xref - - unieuk - - Object associated with a `UNIEUK /(Universal taxonomic framework and integrated reference gene databases for Eukaryotic biology, ecology, and evolution ) `_ record - - A xref is available that links to UNIEUK - * - covid19 - - - - covid19 - - Object associated with covid19 - - - * - covid19Host - - - - covid19Host - - Object associated with a covid19 Host - - +**Pathogen Related Tags** + ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +| tag presentation | high level tag | low level tag | description | comment | ++=====================+================+===================+=======================================================+==============================================+ +|| pathogen || pathogen || Object is some || There will likely be other low level tags to provide || | +|| || || type of pathogen || context. || | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +| pathogen:priority | pathogen | priority | | | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +|| pathogen:bacterium || pathogen || bacterium || Object is of a bacterium organism. || At the time of documentation, the bacterium | +|| || || || || is not specifically pathogenic. | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +|| pathogen:fungus || pathogen || fungus || Object is of a fungus organism. || At the time of documentation, the fungus | +|| || || || || is not specifically pathogenic. | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +|| pathogen:helminth || pathogen || helminth || Object is of a helminth organism. || At the time of documentation, the helminth | +|| || || || || is not specifically pathogenic. | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +|| pathogen:protozoan || pathogen || protozoan || Object is of a protozoan organism. || At the time of documentation, the protozoan | +|| || || || || | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +|| pathogen:virus || pathogen || virus || Object is of a virus organism. || At the time of documentation, the virus | +|| || || || || is not specifically pathogenic. | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +|| datahub:faang || datahub || Faang || Is a Functional Annotation of Animal Genomes project | | +|| || || || `(FAANG) `_ sample | | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +| datahub:metagenome | datahub | metagenome | Is a metagenome and present in that datahub | | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +| covid19 | | covid19 | Object associated with COVID-19 | | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ +| covid19Host | | covid19Host | Object associated with a COVID-19 Host | | ++---------------------+----------------+-------------------+-------------------------------------------------------+----------------------------------------------+ + +**Geographical Tags** + ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| tag presentation | high level tag | low level tag | description | comment | ++========================+==================+===================+=========================================+=========================================+ +| coastal_brackish | coastal_brackish | || Evidence that the object is “coastal || There will likely be other low level | +| | | || or brackish” environment associated. || tags to provide context. | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| coastal_brackish:high | coastal_brackish | high_confidence || Strong evidence that the object is | | +| _confidence | | || “coastal or brackish” environment | | +| | | || associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| coastal_brackish:medium| coastal_brackish | medium_confidence || Moderate evidence that the object is | | +| _confidence | | || “coastal or brackish” environment | | +| | | || associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| coastal_brackish:low_c | coastal_brackish | low_confidence || Weak evidence that the object is | | +| onfidence | | || “coastal or brackish” environment | | +| | | || associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| freshwater | freshwater | || Evidence that it is “freshwater” || There will likely be other low level | +| | | || environment associated || tags to provide context. | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| freshwater:high_confid | freshwater | high_confidence || Strong evidence that the object is | | +| ence | | || freshwater environment associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| freshwater:medium_conf | freshwater | medium_confidence || Moderate evidence that the object is | | +| idence | | || freshwater environment associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| freshwater:low_confide | freshwater | low_confidence || Weak evidence that the object is | | +| nce | | || freshwater environment associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| marine | marine | || Evidence that it is “marine” || There will likely be other low level | +| | | || environment associated. || tags to provide context. | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| marine:high_confidence | marine | high_confidence || Strong evidence that the object is | | +| | | || marine environment associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| marine:medium_confiden | marine | medium_confidence || Moderate evidence that the object is | | +| ce | | || marine environment associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| marine:low_confidence | marine | low_confidence || Weak evidence that the object is | | +| | | || marine environment associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| terrestrial | terrestrial | || Evidence that it is terrestrial(land) || There will likely be other low level | +| | | || environment associated. || tags to provide context. | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| terrestrial:high_confi | terrestrial | high_confidence || Strong evidence that the object is | | +| dence | | || terrestrial(land) environment | | +| | | || associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| terrestrial:medium_con | terrestrial | medium_confidence || Moderate evidence that the object is | | +| fidence | | || terrestrial(land) environment | | +| | | || associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ +| terrestrial:low_confid | terrestrial | low_confidence || Weak evidence that the object is | | +| ence | | || terrestrial(land) environment | | +| | | || associated. | | ++------------------------+------------------+-------------------+-----------------------------------------+-----------------------------------------+ + + +**Cross Reference Tags** + ++------------------------+------------------+-------------------+--------------------------------------------------------+-----------------------------------+ +| tag presentation | high level tag | low level tag | description | comment | ++========================+==================+===================+========================================================+===================================+ +| xref:arrayexpress | xref | arrayexpress || Object associated with an ArrayExpress || A xref is available that links | +| | | || `AE `_ || to ArrayExpress | +| | | || record | | ++------------------------+------------------+-------------------+--------------------------------------------------------+-----------------------------------+ +| xref:europepmc | xref | europepmc || Object associated with a European PubmedCentral || A xref is available that links | +| | | || `EPMC `_ record || to European PubmedCentral | ++------------------------+------------------+-------------------+--------------------------------------------------------+-----------------------------------+ +| xref:pubmed | xref | pubmed || Object associated with an `NCBI Pubmed || A xref is available that links | +| | | || `_ record || to NCBI Pubmed | ++------------------------+------------------+-------------------+--------------------------------------------------------+-----------------------------------+ +| xref:worms | xref | worms || Object associated with a | | +| | | || `WoRMS `_ record | | ++------------------------+------------------+-------------------+--------------------------------------------------------+-----------------------------------+ +| xref:unieuk | xref | unieuk || Object associated with a || A xref is available that links | +| | | || Universal taxonomic framework and integrated || to UNIEUK | +| | | || reference gene databases for Eukaryotic biology, | | +| | | || ecology, and evolution | | +| | | || `(UNIEUK ) `_ record | | ++------------------------+------------------+-------------------+--------------------------------------------------------+-----------------------------------+ + + ------------------------- How are the Tags Created?