From 800d38b8aa0752b5fe3064c77516d49fa4a1ef7f Mon Sep 17 00:00:00 2001 From: Harry Caufield Date: Fri, 6 May 2022 15:59:35 -0400 Subject: [PATCH 1/3] Notes on assembling KG-PHENIO --- download.yaml | 81 ++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 77 insertions(+), 4 deletions(-) diff --git a/download.yaml b/download.yaml index efb13b8..8bad2ad 100644 --- a/download.yaml +++ b/download.yaml @@ -4,6 +4,12 @@ # To add a new item to be download, add a block like this - must have 'url', # 'local_name' is optional, use to avoid name collisions +# This download config retrieves individual PHENIO components, +# in a process similar - but not completely identical - to that +# used by the ODK pipeline. +# See also the PHENIO repo: +# https://github.com/monarch-initiative/phenio + --- # @@ -17,11 +23,78 @@ local_name: robot # -# monarch-merged.owl +# ALL PHENIO PARTS +# as per the phenio ODK config yaml # -- - url: https://data-test.monarchinitiative.org/latest/owl/monarch-merged.owl - local_name: monarch-merged.owl + # products: +# - id: nbo +# use_base: TRUE +# - id: fao +# make_base: TRUE +# - id: oba +# use_base: TRUE +# - id: stato +# - id: bfo +# - id: hsapdv +# make_base: TRUE +# - id: mpath +# make_base: TRUE +# - id: ncbitaxon-taxslim +# mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl +# - id: caro +# make_base: TRUE +# - id: uberon +# use_base: TRUE +# - id: uberon-bridge-to-zfa +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl +# - id: uberon-bridge-to-ma +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl +# - id: uberon-bridge-to-wbbt +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl +# - id: uberon-bridge-to-fbbt +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl +# - id: uberon-bridge-to-fma +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl +# - id: uberon-bridge-to-nifstd +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-nifstd.owl +# - id: cl-bridge-to-ma +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl +# - id: cl-bridge-to-fma +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl +# - id: cl-bridge-to-wbbt +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl +# - id: cl-bridge-to-fbbt +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl +# - id: cl-bridge-to-zfa +# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.owl +# components: +# products: +# - filename: pato.owl +# source: http://purl.obolibrary.org/obo/pato/pato-base.owl +# - filename: go.owl +# source: http://purl.obolibrary.org/obo/go/go-base.owl +# - filename: upheno.owl +# source: https://raw.githubusercontent.com/obophenotype/upheno/master/metazoa.owl +# - filename: mondo-equivalents.owl +# source: http://purl.obolibrary.org/obo/mondo/imports/equivalencies.owl +# - filename: mondo.owl +# source: http://purl.obolibrary.org/obo/mondo/mondo-base.owl +# - filename: eco.owl +# source: http://purl.obolibrary.org/obo/eco/eco-base.owl +# - filename: sepio.owl +# source: http://purl.obolibrary.org/obo/sepio.owl +# - filename: ro.owl +# source: http://purl.obolibrary.org/obo/ro.owl +# - filename: uberon.owl +# source: http://purl.obolibrary.org/obo/uberon/uberon-base.owl +# - filename: fbbt.owl +# source: http://purl.obolibrary.org/obo/fbbt/fbbt-base.owl +# - filename: wbbt.owl +# source: http://purl.obolibrary.org/obo/wbbt/wbbt-base.owl +# - filename: zfa.owl +# source: http://purl.obolibrary.org/obo/zfa/zfa-base.owl +# - filename: chebi.owl +# mirror_from: http://purl.obolibrary.org/obo/chebi.owl.gz # # Current Upheno mappings. From 18557c6b74fa69b3cbd00ccf38b0ee60d03b4eff Mon Sep 17 00:00:00 2001 From: Harry Caufield Date: Fri, 6 May 2022 18:00:48 -0400 Subject: [PATCH 2/3] Adding KG-OBO sources --- download.yaml | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/download.yaml b/download.yaml index 8bad2ad..80053f7 100644 --- a/download.yaml +++ b/download.yaml @@ -26,15 +26,22 @@ # ALL PHENIO PARTS # as per the phenio ODK config yaml # - # products: -# - id: nbo -# use_base: TRUE -# - id: fao -# make_base: TRUE -# - id: oba -# use_base: TRUE -# - id: stato -# - id: bfo +- + url: https://kg-hub.berkeleybop.io/kg-obo/nbo/2021-02-15/nbo_kgx_tsv.tar.gz + local_name: nbo_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/fao/2020-05-07/fao_kgx_tsv.tar.gz + local_name: fao_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/oba/2022-01-19/oba_kgx_tsv.tar.gz + local_name: oba_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/stato/RC1.4/stato_kgx_tsv.tar.gz + local_name: stato_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/bfo/2019-08-26/bfo_kgx_tsv.tar.gz + local_name: bfo_kgx_tsv.tar.gz + # - id: hsapdv # make_base: TRUE # - id: mpath From d7e0e50ec16a9e62a429be5edeab0e36f715bc7a Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Mon, 9 May 2022 11:43:13 -0400 Subject: [PATCH 3/3] Add all PHENIO parts to download config --- download.yaml | 117 ++++++++++++++++++++++++-------------------------- 1 file changed, 55 insertions(+), 62 deletions(-) diff --git a/download.yaml b/download.yaml index 80053f7..9f62059 100644 --- a/download.yaml +++ b/download.yaml @@ -4,7 +4,7 @@ # To add a new item to be download, add a block like this - must have 'url', # 'local_name' is optional, use to avoid name collisions -# This download config retrieves individual PHENIO components, +# This download config retrieves individual PHENIO components, # in a process similar - but not completely identical - to that # used by the ODK pipeline. # See also the PHENIO repo: @@ -24,7 +24,10 @@ # # ALL PHENIO PARTS -# as per the phenio ODK config yaml +# as per the phenio ODK config yaml. +# Note this does not include the bridge files as KGX doesn't +# know what to do with those. +# Same for mondo-equivalents.owl # - url: https://kg-hub.berkeleybop.io/kg-obo/nbo/2021-02-15/nbo_kgx_tsv.tar.gz @@ -41,67 +44,57 @@ - url: https://kg-hub.berkeleybop.io/kg-obo/bfo/2019-08-26/bfo_kgx_tsv.tar.gz local_name: bfo_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/hsapdv/2020-03-10/hsapdv_kgx_tsv.tar.gz + local_name: hsapdv_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/mpath/2020-05-19/mpath_kgx_tsv.tar.gz + local_name: mpath_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/caro/2022-02-18/caro_kgx_tsv.tar.gz + local_name: caro_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/uberon/2022-04-18/uberon_kgx_tsv.tar.gz + local_name: uberon_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/pato/2022-02-20/pato_kgx_tsv.tar.gz + local_name: pato_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/go/2022-03-22/go_kgx_tsv.tar.gz + local_name: go_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/upheno/no_version/upheno_kgx_tsv.tar.gz + local_name: upheno_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/mondo/2022-05-02/mondo_kgx_tsv.tar.gz + local_name: mondo_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/eco/2022-04-11/eco_kgx_tsv.tar.gz + local_name: eco_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/sepio/no_version/sepio_kgx_tsv.tar.gz + local_name: sepio_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/ro/2022-04-25/ro_kgx_tsv.tar.gz + local_name: ro_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/fbbt/2022-04-13/fbbt_kgx_tsv.tar.gz + local_name: fbbt_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/wbbt/2022-03-22/wbbt_kgx_tsv.tar.gz + local_name: wbbt_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/zfa/2022-03-15/zfa_kgx_tsv.tar.gz + local_name: zfa_kgx_tsv.tar.gz +- + url: https://kg-hub.berkeleybop.io/kg-obo/chebi/210/chebi_kgx_tsv.tar.gz + local_name: chebi_kgx_tsv.tar.gz -# - id: hsapdv -# make_base: TRUE -# - id: mpath -# make_base: TRUE -# - id: ncbitaxon-taxslim -# mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -# - id: caro -# make_base: TRUE -# - id: uberon -# use_base: TRUE -# - id: uberon-bridge-to-zfa -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl -# - id: uberon-bridge-to-ma -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl -# - id: uberon-bridge-to-wbbt -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl -# - id: uberon-bridge-to-fbbt -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl -# - id: uberon-bridge-to-fma -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl -# - id: uberon-bridge-to-nifstd -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-nifstd.owl -# - id: cl-bridge-to-ma -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl -# - id: cl-bridge-to-fma -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl -# - id: cl-bridge-to-wbbt -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl -# - id: cl-bridge-to-fbbt -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl -# - id: cl-bridge-to-zfa -# mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.owl -# components: -# products: -# - filename: pato.owl -# source: http://purl.obolibrary.org/obo/pato/pato-base.owl -# - filename: go.owl -# source: http://purl.obolibrary.org/obo/go/go-base.owl -# - filename: upheno.owl -# source: https://raw.githubusercontent.com/obophenotype/upheno/master/metazoa.owl -# - filename: mondo-equivalents.owl -# source: http://purl.obolibrary.org/obo/mondo/imports/equivalencies.owl -# - filename: mondo.owl -# source: http://purl.obolibrary.org/obo/mondo/mondo-base.owl -# - filename: eco.owl -# source: http://purl.obolibrary.org/obo/eco/eco-base.owl -# - filename: sepio.owl -# source: http://purl.obolibrary.org/obo/sepio.owl -# - filename: ro.owl -# source: http://purl.obolibrary.org/obo/ro.owl -# - filename: uberon.owl -# source: http://purl.obolibrary.org/obo/uberon/uberon-base.owl -# - filename: fbbt.owl -# source: http://purl.obolibrary.org/obo/fbbt/fbbt-base.owl -# - filename: wbbt.owl -# source: http://purl.obolibrary.org/obo/wbbt/wbbt-base.owl -# - filename: zfa.owl -# source: http://purl.obolibrary.org/obo/zfa/zfa-base.owl -# - filename: chebi.owl -# mirror_from: http://purl.obolibrary.org/obo/chebi.owl.gz +# NCBI Taxonomy slim +# This isn't on KG-OBO, unlike the above ontologies +- + url: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl + local_name: taxslim.owl # # Current Upheno mappings.