urn-data (#13), HXL-CPLP/forum#50: urn:data:xz:eticaai:ontologia:codi…

…cem:sexum:hl7 added
EticaAI · Apr 28, 2021 · 052e914 · 052e914 · fititnt · Apr 28, 2021
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diff --git a/README.md b/README.md
@@ -128,7 +128,7 @@ _ideal circumstances_ `data global namespace` (the ZZ on
 
 ##### 1.1.3 Ontologia
 
-> **See [ontologia/ontologia](ontologia/ontologia)**
+> **See [ontologia/](ontologia/)**
 
 > "In computer science and information science, an ontology encompasses a
   representation, formal naming and definition of the categories, properties
@@ -138,7 +138,7 @@ _ideal circumstances_ `data global namespace` (the ZZ on
   defining a set of concepts and categories that represent the subject."
   -- [Wikipedia: Ontology (information science)](https://en.wikipedia.org/wiki/Ontology_(information_science)
 
-The contents from [ontologia/ontologia](ontologia/ontologia) both contain some
+The contents from [ontologia/](ontologia/) both contain some
 selected datasets and (while not 100% converted) the main parts of how
 command line tools and libraries released by this repository use.
 

diff --git a/ontologia/cod/README.md b/ontologia/cod/README.md
@@ -1,5 +1,8 @@
 # ontologia/cod: Common Operational Datasets
 
+**Note: the folder ontologia/cod/ do not contain the CODs themselves; This is
+a taxonomy about how to parse COD files, in special COD-AB.**
+
 > This is a DRAFT! (Emerson Rocha, 2021-04-22 21:56 UTC
 
 > Trivia:

diff --git a/ontologia/codicem/TODO.md b/ontologia/codicem/TODO.md
@@ -1,3 +1,5 @@
 > TODO: remove prefix "codicem." from these files so the URN:DATA resolving
         become simpler. Note that there is need to fix symbolic links
         (Emerson Rocha, 2021-04-24 20:52 UTC)
+
+> TODO: link ontologia/iso/iso-iec.5218.hxl.csv to ontologia/codicem/sexum/binarium.hxl.csv (Emerson Rocha, 2021-04-28 03:11 UTC)
diff --git a/ontologia/codicem/anatomiam/README.md b/ontologia/codicem/anatomiam/README.md
@@ -4,7 +4,15 @@
 
 > TODO: place all Terminologia Anatomica codes right after Q Codes (Emerson Rocha, 2021-04-28 01:51 UTC)
 
-See also:
+## terminologia-anatomica.hxl.csv
+- [terminologia-anatomica-EXEMPLUM.hxl.csv](terminologia-anatomica-EXEMPLUM.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:anatomiam:terminologia-anatomica`
+- https://github.com/HXL-CPLP/forum/issues/44
+
+### Build script
+- [make.sh](make.sh)
+
+## See also:
 - **"HXL-CPLP/forum/issues#44: Discussão geral de HXL na área de Medicina Legal (EN: Medical jurisprudence)"**
   - https://github.com/HXL-CPLP/forum/issues/44
 - **"HXL-CPLP/forum/issues#41: HXL-CPLP-Vocab_BRA-policia-judiciaria"**

diff --git a/ontologia/codicem/hxl/standard/core/README.md b/ontologia/codicem/hxl/standard/core/README.md
@@ -0,0 +1,35 @@
+# ontologia/codicem/hxl/standard/core
+
+
+```yaml
+# @see https://data.humdata.org/dataset/hxl-core-schemas
+- urn: "urn:data:xz:hxl:standard:core:hashtag"
+  source:
+    - https://docs.google.com/spreadsheets/d/1En9FlmM8PrbTWgl3UHPF_MXnJ6ziVZFhBbojSJzBdLI/pub?gid=319251406&single=true&output=csv
+
+- urn: "urn:data:xz:hxl:standard:core:attribute"
+  source:
+    - https://docs.google.com/spreadsheets/d/1En9FlmM8PrbTWgl3UHPF_MXnJ6ziVZFhBbojSJzBdLI/pub?gid=1810309357&single=true&output=csv
+```
+
+<!--
+## binarium.hxl.csv
+- [binarium.hxl.csv](binarium.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:sexum:binarium`
+- https://github.com/HXL-CPLP/forum/issues/50
+- https://en.wikipedia.org/wiki/ISO/IEC_5218
+
+## non-binarium.hxl.csv
+- [non-binarium.hxl.csv](non-binarium.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:sexum:non-binarium`
+- https://github.com/HXL-CPLP/forum/issues/50
+- https://en.wikipedia.org/wiki/ISO/IEC_5218
+- https://confluence.hl7.org/display/VOC/Gender+Coding+with+International+Data+Exchange+Standards
+
+## hl7.hxl.csv
+- [hl7.hxl.csv](hl7.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:sexum:hl7`
+- https://github.com/HXL-CPLP/forum/issues/50
+- https://en.wikipedia.org/wiki/ISO/IEC_5218
+- https://confluence.hl7.org/display/VOC/Gender+Coding+with+International+Data+Exchange+Standards
+-->
diff --git a/ontologia/codicem/sexum/README.md b/ontologia/codicem/sexum/README.md
@@ -0,0 +1,23 @@
+# ontologia/codicem/sexum
+
+## binarium.hxl.csv
+- [binarium.hxl.csv](binarium.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:sexum:binarium`
+- https://github.com/HXL-CPLP/forum/issues/50
+- https://en.wikipedia.org/wiki/ISO/IEC_5218
+
+
+## hl7.hxl.csv
+- [hl7.hxl.csv](hl7.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:sexum:hl7`
+- https://github.com/HXL-CPLP/forum/issues/50
+- https://en.wikipedia.org/wiki/ISO/IEC_5218
+- https://confluence.hl7.org/display/VOC/Gender+Coding+with+International+Data+Exchange+Standards
+
+
+## non-binarium.hxl.csv
+- [non-binarium.hxl.csv](non-binarium.hxl.csv)
+- `urn:data:xz:eticaai:ontologia:codicem:sexum:non-binarium`
+- https://github.com/HXL-CPLP/forum/issues/50
+- https://en.wikipedia.org/wiki/ISO/IEC_5218
+- https://confluence.hl7.org/display/VOC/Gender+Coding+with+International+Data+Exchange+Standards
diff --git a/ontologia/codicem/sexum/hl7.hxl.csv b/ontologia/codicem/sexum/hl7.hxl.csv
@@ -0,0 +1,22 @@
+#meta+weka_class,#item+v_iso5218+code,#item+v_iso5218_extended+code,#item+v_us_cdc_sex+code,#meta+raw_netss_ncvhs,#item+meta_rfc4112+v_xz_ecml,#item+v_un_icao_sex+code,#meta+visa_schengen,#item+v_us_naaccr,#item+v_us_census_sex+code,#meta+hl7_v3,#meta+hl7_v2,#meta+x12,#meta+astm,#meta+dicom,#meta+obis,#meta+ubif,#meta+bdt
+not known,0,0,,9,U,X,<,9,,U,U,U,,U,U,?,"U, 0"
+male,1,1,M,1,M,M,M,1,1,M,M,M,M,M,M,m,"M, 1"
+female,2,2,F,2,F,F,F,2,2,F,F,F,F,F,F,f,"W, 2"
+Both (male + female),,,,,,,,,,,,,,,B,,
+Transgender male,,3,,,,,,,,,,,FC,FC,,fc,
+Transgender female,,4,,,,,,,,,,,MC,MC,,mc,
+Transitional,,,,,,,,,,,,,,,T,,
+Not applicable,9,,,,,,,,,,N,,,,,,
+Other,,,O,,,,,3,,,O,,,121102,,,"A, 3"
+Transsexual,,,,,,,,4,,,,,,,,,
+Non-sexed,,,,,,,,,,,,N,,,,,
+Unsexable,,,,,,,,,,,,X,,121103,I,i,
+Unknown sex,,,,,,,,,,,,,U,,,,
+Male pseudohermaphrodite,,,,,,,,,,,,,MP,MP,,,
+Female pseudohermaphrodite,,,,,,,,,,,,,FP,FP,,,
+Hermaprodite,,,,,,,,,,,,,H,H,H,H,
+Simultaneous hermaphrodite,,,,,,,,,,,,,,,,sh,
+Hermaphrodite male phase,,,,,,,,,,,,,,,,Hm,
+Hermaphrodite female phase,,,,,,,,,,,,,,,,hf,
+Ambiguous,,,,,,,,,,,A,,A,121102,,a,
+Mixed sex,,,,,,,,,,,,,,,,x,
diff --git a/ontologia/codicem/sexum/make.sh b/ontologia/codicem/sexum/make.sh
@@ -39,10 +39,9 @@ ONTOLOGIA_CODICEM_SEXUM_NON_BINARIUM="https://proxy.hxlstandard.org/data.csv?des
 # @see https://confluence.hl7.org/display/VOC/Gender+Coding+with+International+Data+Exchange+Standards
 # @see https://docs.google.com/spreadsheets/d/1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k/edit#gid=1946656528
 # @see https://confluence.hl7.org/
+ONTOLOGIA_CODICEM_SEXUM_HL7="https://proxy.hxlstandard.org/data.csv?dest=data_view&url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k%2Fedit%23gid%3D1946656528&filter01=expand&filter-label01=%2Blist+split&strip-headers=on"
 
 # Download terminologia-anatomica.hxl.csv (ignored by .gitignore)
 wget -qO- "$ONTOLOGIA_CODICEM_SEXUM_BINARIUM" > "${ROOTDIR}/ontologia/codicem/sexum/binarium.hxl.csv"
 wget -qO- "$ONTOLOGIA_CODICEM_SEXUM_NON_BINARIUM" > "${ROOTDIR}/ontologia/codicem/sexum/non-binarium.hxl.csv"
-
-# # Get a sample on terminologia-anatomica-EXEMPLUM.hxl.csv
-# cat "${ROOTDIR}/ontologia/codicem/anatomiam/terminologia-anatomica.hxl.csv" | head -n11 > "${ROOTDIR}/ontologia/codicem/anatomiam/terminologia-anatomica-EXEMPLUM.hxl.csv"
+wget -qO- "$ONTOLOGIA_CODICEM_SEXUM_HL7" > "${ROOTDIR}/ontologia/codicem/sexum/hl7.hxl.csv"
diff --git a/ontologia/json/defallo.urn.json b/ontologia/json/defallo.urn.json
@@ -11,6 +11,52 @@
       "https://docs.google.com/spreadsheets/d/1En9FlmM8PrbTWgl3UHPF_MXnJ6ziVZFhBbojSJzBdLI/pub?gid=1810309357&single=true&output=csv"
     ]
   },
+  {
+    "urn": "urn:data:xz:eticaai:ontologia:cod:thesaurum",
+    "source": [
+      "ontologia/cod/thesaurum.hxl.csv",
+      "https://docs.google.com/spreadsheets/d/1NIlLAAhvuotq5QR2vGTrCe1ZuTT_k4vhCoEB3qjo7TU/edit#gid=1204322111"
+    ]
+  },
+  {
+    "urn": "urn:data:xz:eticaai:ontologia:cod:filum-typum",
+    "source": [
+      "ontologia/cod/filum-typum.hxl.csv",
+      "https://docs.google.com/spreadsheets/d/1NIlLAAhvuotq5QR2vGTrCe1ZuTT_k4vhCoEB3qjo7TU/edit#gid=214068544"
+    ]
+  },
+  {
+    "urn": "urn:data:xz:eticaai:ontologia:codicem:anatomiam:terminologia-anatomica",
+    "source": [
+      "ontologia/codicem/anatomiam/terminologia-anatomica.hxl.csv",
+      "ontologia/codicem/anatomiam/terminologia-anatomica-EXEMPLUM.hxl.csv",
+      "https://proxy.hxlstandard.org/data/b02a5f/download/HXL_CPLP-FOD_medicinae-legalis_humana-corpus.csv",
+      "https://docs.google.com/spreadsheets/d/10axnLpDNtAc8Bh921dz5XPXCwo0FUXRcKS6-ermiu5w/edit#gid=1622293684"
+    ]
+  },
+  {
+    "urn": "urn:data:xz:eticaai:ontologia:codicem:sexum:binarium",
+    "source": [
+      "ontologia/codicem/sexum/binarium.hxl.csv",
+      "https://proxy.hxlstandard.org/data.csv?dest=data_edit&strip-headers=on&url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k%2Fedit%23gid%3D214068544",
+      "https://docs.google.com/spreadsheets/d/1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k/edit#gid=214068544"
+    ]
+  },
+  {
+    "urn": "urn:data:xz:eticaai:ontologia:codicem:sexum:hl7",
+    "source": [
+      "ontologia/codicem/sexum/hl7.hxl.csv",
+      "https://docs.google.com/spreadsheets/d/1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k/edit#gid=1946656528"
+    ]
+  },
+  {
+    "urn": "urn:data:xz:eticaai:ontologia:codicem:sexum:non-binarium",
+    "source": [
+      "ontologia/codicem/sexum/non-binarium.hxl.csv",
+      "https://proxy.hxlstandard.org/data.csv?dest=data_edit&filter01=expand&filter-label01=%2Blist+split&strip-headers=on&url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k%2Fedit%23gid%3D530571590",
+      "https://docs.google.com/spreadsheets/d/1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k/edit#gid=530571590"
+    ]
+  },
   {
     "urn": "urn:data:xz:eticaai:ontologia:codicem:linguam",
     "source": [
@@ -39,20 +85,6 @@
       "https://docs.google.com/spreadsheets/d/1B9lzzJC124GvUMbPT-6S9FQiIeO6pHsnHdQib-bcPkg/edit#gid=214068544"
     ]
   },
-  {
-    "urn": "urn:data:xz:eticaai:ontologia:cod:thesaurum",
-    "source": [
-      "ontologia/cod/thesaurum.hxl.csv",
-      "https://docs.google.com/spreadsheets/d/1NIlLAAhvuotq5QR2vGTrCe1ZuTT_k4vhCoEB3qjo7TU/edit#gid=1204322111"
-    ]
-  },
-  {
-    "urn": "urn:data:xz:eticaai:ontologia:cod:filum-typum",
-    "source": [
-      "ontologia/cod/filum-typum.hxl.csv",
-      "https://docs.google.com/spreadsheets/d/1NIlLAAhvuotq5QR2vGTrCe1ZuTT_k4vhCoEB3qjo7TU/edit#gid=214068544"
-    ]
-  },
   {
     "urn": "urn:data:xz:eticaai:cod:ab?fontem",
     "source": [
@@ -86,9 +118,9 @@
     ]
   },
   {
-    "urn": "urn:data:un:cod:ab:{{ISO3166-1}Alpha-3}:adm1.geojson",
+    "urn": "urn:data:un:cod:ab:{[[ISO3166-1]Alpha-3]}:adm1.geojson",
     "source": [
-      "https://beta.itos.uga.edu/CODV2API/api/v1/themes/cod-ab/locations/{{ISO3166-1}Alpha-3}/versions/current/json/1"
+      "https://beta.itos.uga.edu/CODV2API/api/v1/themes/cod-ab/locations/{[ISO3166-1]Alpha-3}/versions/current/json/1"
     ]
   },
   {

diff --git a/ontologia/json/defallo.urn.json.sum b/ontologia/json/defallo.urn.json.sum
@@ -1 +1 @@
-SHA384 (defallo.urn.json) = 5632458ed845407f2de5a2dcbdc26fc8dc13060d880b0716ac78dcb91e7be69f50a53dfbab61207e91f077f8dbf68edf
+SHA384 (defallo.urn.json) = 2a895d9e5bc7c2cd40b3ce0efa842501fbf4522a887ad14b90bfe9f9037eefbf3b8a6544241293a4a4eb34ca4b7bdeb9
diff --git a/ontologia/urn/defallo.urn.yml b/ontologia/urn/defallo.urn.yml
@@ -87,6 +87,11 @@
     - https://proxy.hxlstandard.org/data.csv?dest=data_edit&strip-headers=on&url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k%2Fedit%23gid%3D214068544
     - https://docs.google.com/spreadsheets/d/1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k/edit#gid=214068544
 
+- urn: "urn:data:xz:eticaai:ontologia:codicem:sexum:hl7"
+  source:
+    - ontologia/codicem/sexum/hl7.hxl.csv
+    - https://docs.google.com/spreadsheets/d/1AvYEV8a-X9gZrxrPH0wPgoGHO8ENxWJuVA3z1RpcC5k/edit#gid=1946656528
+
 - urn: "urn:data:xz:eticaai:ontologia:codicem:sexum:non-binarium"
   source:
     - ontologia/codicem/sexum/non-binarium.hxl.csv

diff --git a/ontologia/urn/regulare-expressionem.hxl.csv b/ontologia/urn/regulare-expressionem.hxl.csv
@@ -1,10 +1,10 @@
 #meta+id,#meta+url,#item+id,#vocab+regex+alt,#meta+exemplum,
-ISO3166-1Alpha-2,https://www.iso.org/obp/ui/#search,{{ISO3166-1}Alpha-2},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+v_iso2),"AO, BR, MZ",
-ISO3166-1Alpha-3,https://www.iso.org/obp/ui/#search,{{ISO3166-1}Alpha-3},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+v_iso3),"AGO, BRA, MOZ",
-ISO3166-1Numeric,https://www.iso.org/obp/ui/#search,{{ISO3166-1}Numeric},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+num+v_m49),"024, 076, 508",
-ISO3166-1,https://www.iso.org/obp/ui/#search,{{ISO3166-1}},"urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+v_iso2,country+code+v_iso3,country+code+num+v_m49)","024, AO, AGO, 076, BR, BRA, 508, MZ, MOZ",
-UNM49,https://en.wikipedia.org/wiki/UN_M49,{{UNM49}},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=code+num+v_m49),"024, 076, 508",
-ISO3166-1Emoji,https://emojipedia.org/flags/,{{ISO3166-1}Emoji},,"🇦🇴, 🇧🇷, 🇲🇿",
-ISO15924Special,https://en.wikipedia.org/wiki/ISO_15924,{{ISO15924}Special},urn:data:xz:eticaai:ontologia:codicem:scriptum?=|$(hxlcut --include=vocab+code+v_iso15924+text),"Arab, Cyrl, Hans, Hant, Latn",
-ISO15924Numeric,https://en.wikipedia.org/wiki/ISO_15924,{{ISO15924}Numeric},urn:data:xz:eticaai:ontologia:codicem:scriptum?=|$(hxlcut --include=vocab+code+v_iso15924+number),"160, 220, 501, 502, 215",
-ISO15924,https://en.wikipedia.org/wiki/ISO_15924,{{ISO15924}},"urn:data:xz:eticaai:ontologia:codicem:scriptum?=|$(hxlcut --include=vocab+code+v_iso15924+text,vocab+code+v_iso15924+number)","Arab, 160, Cyrl, 220, Hans, 501, Hant, 502, Latn, 215",
+ISO3166-1Alpha-2,https://www.iso.org/obp/ui/#search,{[ISO3166-1]Alpha-2},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+v_iso2),"AO, BR, MZ",
+ISO3166-1Alpha-3,https://www.iso.org/obp/ui/#search,{[ISO3166-1]Alpha-3},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+v_iso3),"AGO, BRA, MOZ",
+ISO3166-1Numeric,https://www.iso.org/obp/ui/#search,{[ISO3166-1]Numeric},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+num+v_m49),"024, 076, 508",
+ISO3166-1,https://www.iso.org/obp/ui/#search,{[ISO3166-1]},"urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=country+code+v_iso2,country+code+v_iso3,country+code+num+v_m49)","024, AO, AGO, 076, BR, BRA, 508, MZ, MOZ",
+UNM49,https://en.wikipedia.org/wiki/UN_M49,{[UNM49]},urn:data:xz:eticaai:ontologia:codicem:locum?=|$(hxlcut --include=code+num+v_m49),"024, 076, 508",
+ISO3166-1Emoji,https://emojipedia.org/flags/,{[ISO3166-1]Emoji},,"🇦🇴, 🇧🇷, 🇲🇿",
+ISO15924Special,https://en.wikipedia.org/wiki/ISO_15924,{[ISO15924]Special},urn:data:xz:eticaai:ontologia:codicem:scriptum?=|$(hxlcut --include=vocab+code+v_iso15924+text),"Arab, Cyrl, Hans, Hant, Latn",
+ISO15924Numeric,https://en.wikipedia.org/wiki/ISO_15924,{[ISO15924]Numeric},urn:data:xz:eticaai:ontologia:codicem:scriptum?=|$(hxlcut --include=vocab+code+v_iso15924+number),"160, 220, 501, 502, 215",
+ISO15924,https://en.wikipedia.org/wiki/ISO_15924,{[ISO15924]},"urn:data:xz:eticaai:ontologia:codicem:scriptum?=|$(hxlcut --include=vocab+code+v_iso15924+text,vocab+code+v_iso15924+number)","Arab, 160, Cyrl, 220, Hans, 501, Hant, 502, Latn, 215",
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		SHA384 (defallo.urn.json) = 5632458ed845407f2de5a2dcbdc26fc8dc13060d880b0716ac78dcb91e7be69f50a53dfbab61207e91f077f8dbf68edf
		SHA384 (defallo.urn.json) = 2a895d9e5bc7c2cd40b3ce0efa842501fbf4522a887ad14b90bfe9f9037eefbf3b8a6544241293a4a4eb34ca4b7bdeb9