diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt index f89327a..c468889 100644 --- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt +++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt @@ -34,6 +34,7 @@ exclude-result-prefixes="xsl md panxslt set"> + @@ -231,6 +232,25 @@ exclude-result-prefixes="xsl md panxslt set"> + + + + + + + + + + + + + + + + + + + diff --git a/transformations/abcd2bioschemas/abcd2bioschemas.ipynb b/transformations/abcd2bioschemas/abcd2bioschemas.ipynb index 051a7cb..eacb752 100644 --- a/transformations/abcd2bioschemas/abcd2bioschemas.ipynb +++ b/transformations/abcd2bioschemas/abcd2bioschemas.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 13, + "execution_count": 1, "id": "71bcacf7", "metadata": {}, "outputs": [ @@ -11,7 +11,7 @@ "output_type": "stream", "text": [ "Defaulting to user installation because normal site-packages is not writeable\n", - "Requirement already satisfied: saxonche in c:\\users\\fichtmueller\\appdata\\roaming\\python\\python311\\site-packages (12.4.1.0)\n" + "Requirement already satisfied: saxonche in c:\\users\\mernst\\appdata\\roaming\\python\\python39\\site-packages (12.4.2)\n" ] }, { @@ -19,7 +19,7 @@ "output_type": "stream", "text": [ "\n", - "[notice] A new release of pip is available: 23.3.2 -> 24.0\n", + "[notice] A new release of pip is available: 23.1.2 -> 24.0\n", "[notice] To update, run: python.exe -m pip install --upgrade pip\n" ] }, @@ -28,7 +28,7 @@ "output_type": "stream", "text": [ "Defaulting to user installation because normal site-packages is not writeable\n", - "Requirement already satisfied: xmltodict in c:\\users\\fichtmueller\\appdata\\roaming\\python\\python311\\site-packages (0.12.0)\n" + "Requirement already satisfied: xmltodict in c:\\users\\mernst\\appdata\\roaming\\python\\python39\\site-packages (0.13.0)\n" ] }, { @@ -36,7 +36,7 @@ "output_type": "stream", "text": [ "\n", - "[notice] A new release of pip is available: 23.3.2 -> 24.0\n", + "[notice] A new release of pip is available: 23.1.2 -> 24.0\n", "[notice] To update, run: python.exe -m pip install --upgrade pip\n" ] } @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 1, "id": "c16196d8", "metadata": {}, "outputs": [], @@ -60,7 +60,7 @@ }, { "cell_type": "code", - "execution_count": 40, + "execution_count": 2, "id": "0784e107", "metadata": {}, "outputs": [], @@ -72,16 +72,18 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 3, "id": "daebdd55", - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Test SaxonC on Python\n", - "SaxonC-HE 12.4 from Saxonica\n" + "SaxonC-HE 12.4.2 from Saxonica\n" ] } ], @@ -95,17 +97,17 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": 4, "id": "1daebf42", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "'\\n\\n https://data.bgbm.org/dataset/gfbio/0004/\\n Plants at Crater Road of Queen Elizabeth National Park, Uganda.\\n https://data.bgbm.org/dataset/gfbio/0004/\\n Plant occurrences at Crater Road, Queen Elizabeth National Park, Uganda (April 1995 until March 1997). Project data from Dr. Anke Hoffmann, supplementary data of the dissertation: \"Hoffmann, Anke (1999). Habitat use and population dynamics of small mammals in the grasslands of the Queen Elizabeth National Park, Uganda. Dissertation Technische Universität Carolo-Wilhelmina zu Braunschweig. Braunschweig.\" This dataset was mobilized in co-operation with the DFG-funded project reBiND (http://rebind.bgbm.org/). The following Abstract describes the dissertation: In the grasslands of Queen Elizabeth National Park in Uganda small mammal populations were studied between April 1995 and March 1997 using the capture-mark-release-method and radio-telemetry. The 6 study plots were situated in the Imperata-Cymbopogon-grassland and in the bushland-grassland-mosaic and differed mainly in vegetation, habitat structures, cover and grazing pressure due to big game. The effect of fire was an important aspect to all questions of the study. In total 5.702 catches including 1.295 individuals out of 20 species of the families Muridae (12), Myoxidae (1) und Soricidae (7) were recorded in 65 trapping sessions. The most abundant species were Lemniscomys striatus, Mastomys natalensis and Arvicanthis nairobae. For all plots zoocoenosis and dominance structures are described as well as similarity of fauna and species diversity are compared. The population structures of the 3 most common species are compared in 2 plots of their highest abundance. Emphasis of the investigation is laid on the population development, sex ratio, weight and reproduction. Beyond the survival and turnover rates are determined for these populations. For all species habitat preferences are described. The range lenghts of L. striatus and M. natalensis were ascertained for different plots. Their dependence of population density, sex, sexual activity, body weight, rainfall and bush fire is revised. In all 9 L. striatus, 7 M. natalensis and 8 A. nairobae were radio-tracked successfully and their home range sizes, utilization patterns and activities investigated. For these species an inverse relationship between home range size and population density exists.\\n en\\n HumanObservation\\n 1999-10-19\\n 2018-01-22\\n 2018-01-22\\n \\n true\\n \\n 267\\n records\\n \\n \\n CC BY 4.0\\n \\n \\n \\n Uganda\\n UG \\n \\n 1995-06-13/1997-03-13\\n \\n Aristida adscensionis\\n Species\\n \\n \\n Bothriochloa insculpta\\n Species\\n \\n \\n Cenchrus ciliaris\\n Species\\n \\n \\n Chloris gayana\\n Species\\n \\n \\n Sporobolus pyramidalis\\n Species\\n \\n \\n Themeda triandra\\n Species\\n \\n \\n Sida ovata\\n Species\\n \\n \\n Acacia hockii\\n Species\\n \\n \\n Achyranthes aspera\\n Species\\n \\n \\n Capparis tomentosa\\n Species\\n \\n \\n Erythrococca bongensis\\n Species\\n \\n \\n Euphorbia candelabrum\\n Species\\n \\n \\n Flueggea virosa\\n Species\\n \\n \\n Hoslundia opposita\\n Species\\n \\n \\n Ocimum suave\\n Species\\n \\n \\n Abutilon guineense\\n Species\\n \\n \\n Grewia similis\\n Species\\n \\n \\n Cissus quadrangularis\\n Species\\n \\n \\n Hyperthelia dissoluta\\n Species\\n \\n \\n Hyparrhenia rufa\\n Species\\n \\n \\n Abutilon hirtum\\n Species\\n \\n \\n Lantana camara\\n Species\\n \\n \\n Euphorbia hirta\\n Species\\n \\n \\n Indigofera simplicifolia\\n Species\\n \\n \\n Indigofera spicata\\n Species\\n \\n \\n Tephrosia nana\\n Species\\n \\n \\n Vigna ambacensis\\n Species\\n \\n \\n Lantana trifolia\\n Species\\n \\n \\n Solanum incanum\\n Species\\n \\n \\n Conyza stricta\\n Species\\n \\n \\n Panicum maximum\\n Species\\n \\n \\n Turraea robusta\\n Species\\n \\n \\n Acacia sieberiana\\n Species\\n \\n \\n Tarenna graveolens\\n Species\\n \\n \\n Cissus ovata\\n Species\\n \\n \\n Brachiaria eminii\\n Species\\n \\n \\n Indigofera arrecta\\n Species\\n \\n \\n Leonotis nepetifolia\\n Species\\n \\n \\n Leucas martinicensis\\n Species\\n \\n \\n Hibiscus aethiopicus\\n Species\\n \\n \\n Cissus rotundifolia\\n Species\\n \\n \\n Heteropogon contortus\\n Species\\n \\n \\n Cayratia ibuensis\\n Species\\n \\n \\n Maerua triphylla\\n Species\\n \\n \\n Hibiscus aponeurus\\n Species\\n \\n \\n Piper sp.\\n Species\\n \\n \\n Pavetta albertina\\n Species\\n \\n \\n Plantae\\n regnum\\n \\n \\n Gramineae\\n familia\\n \\n \\n Malvaceae\\n familia\\n \\n \\n Mimosaceae\\n familia\\n \\n \\n Amaranthaceae\\n familia\\n \\n \\n Capparidaceae\\n familia\\n \\n \\n Euphorbiaceae\\n familia\\n \\n \\n Labiatae\\n familia\\n \\n \\n Tiliaceae\\n familia\\n \\n \\n Vitaceae\\n familia\\n \\n \\n Verbenaceae\\n familia\\n \\n \\n Papilioniaceae\\n familia\\n \\n \\n Solanaceae\\n familia\\n \\n \\n Compositae\\n familia\\n \\n \\n Meliaceae\\n familia\\n \\n \\n Rubiaceae\\n familia\\n \\n \\n Piperaceae\\n familia\\n \\n \\n Aristida adscensionis\\n Species\\n \\n \\n Bothriochloa insculpta\\n Species\\n \\n \\n Cenchrus ciliaris\\n Species\\n \\n \\n Chloris gayana\\n Species\\n \\n \\n Sporobolus pyramidalis\\n Species\\n \\n \\n Themeda triandra\\n Species\\n \\n \\n Sida ovata\\n Species\\n \\n \\n Acacia hockii\\n Species\\n \\n \\n Achyranthes aspera\\n Species\\n \\n \\n Capparis tomentosa\\n Species\\n \\n \\n Erythrococca bongensis\\n Species\\n \\n \\n Euphorbia candelabrum\\n Species\\n \\n \\n Flueggea virosa\\n Species\\n \\n \\n Hoslundia opposita\\n Species\\n \\n \\n Ocimum suave\\n Species\\n \\n \\n Abutilon guineense\\n Species\\n \\n \\n Grewia similis\\n Species\\n \\n \\n Cissus quadrangularis\\n Species\\n \\n \\n Hyperthelia dissoluta\\n Species\\n \\n \\n Hyparrhenia rufa\\n Species\\n \\n \\n Abutilon hirtum\\n Species\\n \\n \\n Lantana camara\\n Species\\n \\n \\n Euphorbia hirta\\n Species\\n \\n \\n Indigofera simplicifolia\\n Species\\n \\n \\n Indigofera spicata\\n Species\\n \\n \\n Tephrosia nana\\n Species\\n \\n \\n Vigna ambacensis\\n Species\\n \\n \\n Lantana trifolia\\n Species\\n \\n \\n Solanum incanum\\n Species\\n \\n \\n Conyza stricta\\n Species\\n \\n \\n Panicum maximum\\n Species\\n \\n \\n Turraea robusta\\n Species\\n \\n \\n Acacia sieberiana\\n Species\\n \\n \\n Tarenna graveolens\\n Species\\n \\n \\n Cissus ovata\\n Species\\n \\n \\n Brachiaria eminii\\n Species\\n \\n \\n Indigofera arrecta\\n Species\\n \\n \\n Leonotis nepetifolia\\n Species\\n \\n \\n Leucas martinicensis\\n Species\\n \\n \\n Hibiscus aethiopicus\\n Species\\n \\n \\n Cissus rotundifolia\\n Species\\n \\n \\n Heteropogon contortus\\n Species\\n \\n \\n Cayratia ibuensis\\n Species\\n \\n \\n Maerua triphylla\\n Species\\n \\n \\n Hibiscus aponeurus\\n Species\\n \\n \\n Piper sp.\\n Species\\n \\n \\n Pavetta albertina\\n Species\\n \\n \\n GFBio Data Center BGBM\\n gfbio@bgbm.org\\n
Königin-Luise-Str.6-8, 14195 Berlin, Germany
\\n \\n \\n GFBio Data Center BGBM\\n gfbio@bgbm.org\\n
Königin-Luise-Str.6-8, 14195 Berlin, Germany
\\n \\n \\n Tom Friday Baluku, Maren Gleisberg\\n \\n\\n'" + "'\\n\\n https://data.bgbm.org/dataset/gfbio/0004/\\n Plants at Crater Road of Queen Elizabeth National Park, Uganda.\\n https://data.bgbm.org/dataset/gfbio/0004/\\n Plant occurrences at Crater Road, Queen Elizabeth National Park, Uganda (April 1995 until March 1997). Project data from Dr. Anke Hoffmann, supplementary data of the dissertation: \"Hoffmann, Anke (1999). Habitat use and population dynamics of small mammals in the grasslands of the Queen Elizabeth National Park, Uganda. Dissertation Technische Universität Carolo-Wilhelmina zu Braunschweig. Braunschweig.\" This dataset was mobilized in co-operation with the DFG-funded project reBiND (http://rebind.bgbm.org/). The following Abstract describes the dissertation: In the grasslands of Queen Elizabeth National Park in Uganda small mammal populations were studied between April 1995 and March 1997 using the capture-mark-release-method and radio-telemetry. The 6 study plots were situated in the Imperata-Cymbopogon-grassland and in the bushland-grassland-mosaic and differed mainly in vegetation, habitat structures, cover and grazing pressure due to big game. The effect of fire was an important aspect to all questions of the study. In total 5.702 catches including 1.295 individuals out of 20 species of the families Muridae (12), Myoxidae (1) und Soricidae (7) were recorded in 65 trapping sessions. The most abundant species were Lemniscomys striatus, Mastomys natalensis and Arvicanthis nairobae. For all plots zoocoenosis and dominance structures are described as well as similarity of fauna and species diversity are compared. The population structures of the 3 most common species are compared in 2 plots of their highest abundance. Emphasis of the investigation is laid on the population development, sex ratio, weight and reproduction. Beyond the survival and turnover rates are determined for these populations. For all species habitat preferences are described. The range lenghts of L. striatus and M. natalensis were ascertained for different plots. Their dependence of population density, sex, sexual activity, body weight, rainfall and bush fire is revised. In all 9 L. striatus, 7 M. natalensis and 8 A. nairobae were radio-tracked successfully and their home range sizes, utilization patterns and activities investigated. For these species an inverse relationship between home range size and population density exists.\\n en\\n HumanObservation\\n 1999-10-19\\n 2018-01-22\\n 2018-01-22\\n \\n true\\n \\n 267\\n records\\n \\n \\n CC BY 4.0\\n \\n \\n \\n Uganda\\n UG \\n \\n 1995-06-13/1997-03-13\\n \\n \\n Publication 1 citing this record\\n Aristida adscensionis cited from Hoffmann\\n https://data-rebind.bgbm.org/gfbio/biocase/pub1\\n \\n \\n Publication 2 citing this record\\n Aristida adscensionis cited from Hoffmann\\n https://data-rebind.bgbm.org/gfbio/biocase/pub2\\n \\n \\n Publication 1 citing this record\\n Bothriochloa insculpta cited from Hoffmann\\n https://data-rebind.bgbm.org/gfbio/biocase/pub1\\n \\n \\n Publication 2 citing this record\\n Bothriochloa insculpta cited from Hoffmann\\n https://data-rebind.bgbm.org/gfbio/biocase/pub2\\n \\n \\n \\n Aristida adscensionis\\n Species\\n \\n \\n Bothriochloa insculpta\\n Species\\n \\n \\n Cenchrus ciliaris\\n Species\\n \\n \\n Chloris gayana\\n Species\\n \\n \\n Sporobolus pyramidalis\\n Species\\n \\n \\n Themeda triandra\\n Species\\n \\n \\n Sida ovata\\n Species\\n \\n \\n Acacia hockii\\n Species\\n \\n \\n Achyranthes aspera\\n Species\\n \\n \\n Capparis tomentosa\\n Species\\n \\n \\n Erythrococca bongensis\\n Species\\n \\n \\n Euphorbia candelabrum\\n Species\\n \\n \\n Flueggea virosa\\n Species\\n \\n \\n Hoslundia opposita\\n Species\\n \\n \\n Ocimum suave\\n Species\\n \\n \\n Abutilon guineense\\n Species\\n \\n \\n Grewia similis\\n Species\\n \\n \\n Cissus quadrangularis\\n Species\\n \\n \\n Hyperthelia dissoluta\\n Species\\n \\n \\n Hyparrhenia rufa\\n Species\\n \\n \\n Abutilon hirtum\\n Species\\n \\n \\n Lantana camara\\n Species\\n \\n \\n Euphorbia hirta\\n Species\\n \\n \\n Indigofera simplicifolia\\n Species\\n \\n \\n Indigofera spicata\\n Species\\n \\n \\n Tephrosia nana\\n Species\\n \\n \\n Vigna ambacensis\\n Species\\n \\n \\n Lantana trifolia\\n Species\\n \\n \\n Solanum incanum\\n Species\\n \\n \\n Conyza stricta\\n Species\\n \\n \\n Panicum maximum\\n Species\\n \\n \\n Turraea robusta\\n Species\\n \\n \\n Acacia sieberiana\\n Species\\n \\n \\n Tarenna graveolens\\n Species\\n \\n \\n Cissus ovata\\n Species\\n \\n \\n Brachiaria eminii\\n Species\\n \\n \\n Indigofera arrecta\\n Species\\n \\n \\n Leonotis nepetifolia\\n Species\\n \\n \\n Leucas martinicensis\\n Species\\n \\n \\n Hibiscus aethiopicus\\n Species\\n \\n \\n Cissus rotundifolia\\n Species\\n \\n \\n Heteropogon contortus\\n Species\\n \\n \\n Cayratia ibuensis\\n Species\\n \\n \\n Maerua triphylla\\n Species\\n \\n \\n Hibiscus aponeurus\\n Species\\n \\n \\n Piper sp.\\n Species\\n \\n \\n Pavetta albertina\\n Species\\n \\n \\n Plantae\\n regnum\\n \\n \\n Gramineae\\n familia\\n \\n \\n Malvaceae\\n familia\\n \\n \\n Mimosaceae\\n familia\\n \\n \\n Amaranthaceae\\n familia\\n \\n \\n Capparidaceae\\n familia\\n \\n \\n Euphorbiaceae\\n familia\\n \\n \\n Labiatae\\n familia\\n \\n \\n Tiliaceae\\n familia\\n \\n \\n Vitaceae\\n familia\\n \\n \\n Verbenaceae\\n familia\\n \\n \\n Papilioniaceae\\n familia\\n \\n \\n Solanaceae\\n familia\\n \\n \\n Compositae\\n familia\\n \\n \\n Meliaceae\\n familia\\n \\n \\n Rubiaceae\\n familia\\n \\n \\n Piperaceae\\n familia\\n \\n \\n Aristida adscensionis\\n Species\\n \\n \\n Bothriochloa insculpta\\n Species\\n \\n \\n Cenchrus ciliaris\\n Species\\n \\n \\n Chloris gayana\\n Species\\n \\n \\n Sporobolus pyramidalis\\n Species\\n \\n \\n Themeda triandra\\n Species\\n \\n \\n Sida ovata\\n Species\\n \\n \\n Acacia hockii\\n Species\\n \\n \\n Achyranthes aspera\\n Species\\n \\n \\n Capparis tomentosa\\n Species\\n \\n \\n Erythrococca bongensis\\n Species\\n \\n \\n Euphorbia candelabrum\\n Species\\n \\n \\n Flueggea virosa\\n Species\\n \\n \\n Hoslundia opposita\\n Species\\n \\n \\n Ocimum suave\\n Species\\n \\n \\n Abutilon guineense\\n Species\\n \\n \\n Grewia similis\\n Species\\n \\n \\n Cissus quadrangularis\\n Species\\n \\n \\n Hyperthelia dissoluta\\n Species\\n \\n \\n Hyparrhenia rufa\\n Species\\n \\n \\n Abutilon hirtum\\n Species\\n \\n \\n Lantana camara\\n Species\\n \\n \\n Euphorbia hirta\\n Species\\n \\n \\n Indigofera simplicifolia\\n Species\\n \\n \\n Indigofera spicata\\n Species\\n \\n \\n Tephrosia nana\\n Species\\n \\n \\n Vigna ambacensis\\n Species\\n \\n \\n Lantana trifolia\\n Species\\n \\n \\n Solanum incanum\\n Species\\n \\n \\n Conyza stricta\\n Species\\n \\n \\n Panicum maximum\\n Species\\n \\n \\n Turraea robusta\\n Species\\n \\n \\n Acacia sieberiana\\n Species\\n \\n \\n Tarenna graveolens\\n Species\\n \\n \\n Cissus ovata\\n Species\\n \\n \\n Brachiaria eminii\\n Species\\n \\n \\n Indigofera arrecta\\n Species\\n \\n \\n Leonotis nepetifolia\\n Species\\n \\n \\n Leucas martinicensis\\n Species\\n \\n \\n Hibiscus aethiopicus\\n Species\\n \\n \\n Cissus rotundifolia\\n Species\\n \\n \\n Heteropogon contortus\\n Species\\n \\n \\n Cayratia ibuensis\\n Species\\n \\n \\n Maerua triphylla\\n Species\\n \\n \\n Hibiscus aponeurus\\n Species\\n \\n \\n Piper sp.\\n Species\\n \\n \\n Pavetta albertina\\n Species\\n \\n \\n GFBio Data Center BGBM\\n gfbio@bgbm.org\\n
Königin-Luise-Str.6-8, 14195 Berlin, Germany
\\n \\n \\n GFBio Data Center BGBM\\n gfbio@bgbm.org\\n
Königin-Luise-Str.6-8, 14195 Berlin, Germany
\\n \\n \\n Tom Friday Baluku, Maren Gleisberg\\n \\n\\n'" ] }, - "execution_count": 41, + "execution_count": 4, "metadata": {}, "output_type": "execute_result" } @@ -120,401 +122,185 @@ }, { "cell_type": "code", - "execution_count": 51, + "execution_count": 5, "id": "de5ebfe4", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "OrderedDict([('@xmlns:abcd', 'http://www.tdwg.org/schemas/abcd/2.06'),\n", - " ('@xmlns:efg', 'http://www.synthesys.info/ABCDEFG/1.0'),\n", - " ('@xmlns:xs', 'http://www.w3.org/2001/XMLSchema'),\n", - " ('@xmlns:xsi', 'http://www.w3.org/2001/XMLSchema-instance'),\n", - " ('@context', 'http://schema.org/'),\n", - " ('@type', 'Dataset'),\n", - " ('@id', 'https://data.bgbm.org/dataset/gfbio/0004/'),\n", - " ('id', 'https://data.bgbm.org/dataset/gfbio/0004/'),\n", - " ('name',\n", - " 'Plants at Crater Road of Queen Elizabeth National Park, Uganda.'),\n", - " ('url', 'https://data.bgbm.org/dataset/gfbio/0004/'),\n", - " ('description',\n", - " 'Plant occurrences at Crater Road, Queen Elizabeth National Park, Uganda (April 1995 until March 1997). Project data from Dr. Anke Hoffmann, supplementary data of the dissertation: \"Hoffmann, Anke (1999). Habitat use and population dynamics of small mammals in the grasslands of the Queen Elizabeth National Park, Uganda. Dissertation Technische Universität Carolo-Wilhelmina zu Braunschweig. Braunschweig.\" This dataset was mobilized in co-operation with the DFG-funded project reBiND (http://rebind.bgbm.org/). The following Abstract describes the dissertation: In the grasslands of Queen Elizabeth National Park in Uganda small mammal populations were studied between April 1995 and March 1997 using the capture-mark-release-method and radio-telemetry. The 6 study plots were situated in the Imperata-Cymbopogon-grassland and in the bushland-grassland-mosaic and differed mainly in vegetation, habitat structures, cover and grazing pressure due to big game. The effect of fire was an important aspect to all questions of the study. In total 5.702 catches including 1.295 individuals out of 20 species of the families Muridae (12), Myoxidae (1) und Soricidae (7) were recorded in 65 trapping sessions. The most abundant species were Lemniscomys striatus, Mastomys natalensis and Arvicanthis nairobae. For all plots zoocoenosis and dominance structures are described as well as similarity of fauna and species diversity are compared. The population structures of the 3 most common species are compared in 2 plots of their highest abundance. Emphasis of the investigation is laid on the population development, sex ratio, weight and reproduction. Beyond the survival and turnover rates are determined for these populations. For all species habitat preferences are described. The range lenghts of L. striatus and M. natalensis were ascertained for different plots. Their dependence of population density, sex, sexual activity, body weight, rainfall and bush fire is revised. In all 9 L. striatus, 7 M. natalensis and 8 A. nairobae were radio-tracked successfully and their home range sizes, utilization patterns and activities investigated. For these species an inverse relationship between home range size and population density exists.'),\n", - " ('inLanguage', 'en'),\n", - " ('additionalType', 'HumanObservation'),\n", - " ('dateCreated', '1999-10-19'),\n", - " ('dateModified', '2018-01-22'),\n", - " ('datePublished', '2018-01-22'),\n", - " ('distribution', None),\n", - " ('isAccessibleForFree',\n", - " OrderedDict([('@xsi:type', 'xs:boolean'), ('#text', 'true')])),\n", - " ('size',\n", - " OrderedDict([('@type', 'QuantitativeValue'),\n", - " ('value',\n", - " OrderedDict([('@xsi:type', 'xs:int'),\n", - " ('#text', '267')])),\n", - " ('unitText', 'records')])),\n", - " ('license',\n", - " OrderedDict([('@type', 'CreativeWork'),\n", - " ('name', 'CC BY 4.0'),\n", - " ('description', None)])),\n", - " ('spatialCoverage',\n", - " OrderedDict([('@type', 'Country'),\n", - " ('name', 'Uganda'),\n", - " ('identifier', 'UG')])),\n", - " ('temporalCoverage', '1995-06-13/1997-03-13'),\n", - " ('about',\n", - " [OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Aristida adscensionis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Bothriochloa insculpta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cenchrus ciliaris'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Chloris gayana'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Sporobolus pyramidalis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Themeda triandra'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Sida ovata'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Acacia hockii'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Achyranthes aspera'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Capparis tomentosa'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Erythrococca bongensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Euphorbia candelabrum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Flueggea virosa'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hoslundia opposita'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Ocimum suave'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Abutilon guineense'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Grewia similis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cissus quadrangularis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hyperthelia dissoluta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hyparrhenia rufa'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Abutilon hirtum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Lantana camara'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Euphorbia hirta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Indigofera simplicifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Indigofera spicata'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Tephrosia nana'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Vigna ambacensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Lantana trifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Solanum incanum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Conyza stricta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Panicum maximum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Turraea robusta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Acacia sieberiana'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Tarenna graveolens'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cissus ovata'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Brachiaria eminii'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Indigofera arrecta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Leonotis nepetifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Leucas martinicensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hibiscus aethiopicus'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cissus rotundifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Heteropogon contortus'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cayratia ibuensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Maerua triphylla'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hibiscus aponeurus'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Piper sp.'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Pavetta albertina'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Plantae'),\n", - " ('taxonRank', 'regnum')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Gramineae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Malvaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Mimosaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Amaranthaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Capparidaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Euphorbiaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Labiatae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Tiliaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Vitaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Verbenaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Papilioniaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Solanaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Compositae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Meliaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Rubiaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Piperaceae'),\n", - " ('taxonRank', 'familia')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Aristida adscensionis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Bothriochloa insculpta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cenchrus ciliaris'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Chloris gayana'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Sporobolus pyramidalis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Themeda triandra'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Sida ovata'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Acacia hockii'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Achyranthes aspera'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Capparis tomentosa'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Erythrococca bongensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Euphorbia candelabrum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Flueggea virosa'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hoslundia opposita'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Ocimum suave'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Abutilon guineense'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Grewia similis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cissus quadrangularis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hyperthelia dissoluta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hyparrhenia rufa'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Abutilon hirtum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Lantana camara'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Euphorbia hirta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Indigofera simplicifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Indigofera spicata'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Tephrosia nana'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Vigna ambacensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Lantana trifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Solanum incanum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Conyza stricta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Panicum maximum'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Turraea robusta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Acacia sieberiana'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Tarenna graveolens'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cissus ovata'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Brachiaria eminii'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Indigofera arrecta'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Leonotis nepetifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Leucas martinicensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hibiscus aethiopicus'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cissus rotundifolia'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Heteropogon contortus'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Cayratia ibuensis'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Maerua triphylla'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Hibiscus aponeurus'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Piper sp.'),\n", - " ('taxonRank', 'Species')]),\n", - " OrderedDict([('@type', 'Taxon'),\n", - " ('name', 'Pavetta albertina'),\n", - " ('taxonRank', 'Species')])]),\n", - " ('publisher',\n", - " OrderedDict([('@type', 'Organization'),\n", - " ('name', 'GFBio Data Center BGBM'),\n", - " ('email', 'gfbio@bgbm.org'),\n", - " ('address',\n", - " 'Königin-Luise-Str.6-8, 14195 Berlin, Germany')])),\n", - " ('maintainer',\n", - " OrderedDict([('@type', 'Organization'),\n", - " ('name', 'GFBio Data Center BGBM'),\n", - " ('email', 'gfbio@bgbm.org'),\n", - " ('address',\n", - " 'Königin-Luise-Str.6-8, 14195 Berlin, Germany')])),\n", - " ('contributor',\n", - " OrderedDict([('@type', 'Person'),\n", - " ('name', 'Tom Friday Baluku, Maren Gleisberg')]))])" + "{'@xmlns:abcd': 'http://www.tdwg.org/schemas/abcd/2.06',\n", + " '@xmlns:efg': 'http://www.synthesys.info/ABCDEFG/1.0',\n", + " '@xmlns:xs': 'http://www.w3.org/2001/XMLSchema',\n", + " '@xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',\n", + " '@context': 'http://schema.org/',\n", + " '@type': 'Dataset',\n", + " '@id': 'https://data.bgbm.org/dataset/gfbio/0004/',\n", + " 'id': 'https://data.bgbm.org/dataset/gfbio/0004/',\n", + " 'name': 'Plants at Crater Road of Queen Elizabeth National Park, Uganda.',\n", + " 'url': 'https://data.bgbm.org/dataset/gfbio/0004/',\n", + " 'description': 'Plant occurrences at Crater Road, Queen Elizabeth National Park, Uganda (April 1995 until March 1997). Project data from Dr. Anke Hoffmann, supplementary data of the dissertation: \"Hoffmann, Anke (1999). Habitat use and population dynamics of small mammals in the grasslands of the Queen Elizabeth National Park, Uganda. Dissertation Technische Universität Carolo-Wilhelmina zu Braunschweig. Braunschweig.\" This dataset was mobilized in co-operation with the DFG-funded project reBiND (http://rebind.bgbm.org/). The following Abstract describes the dissertation: In the grasslands of Queen Elizabeth National Park in Uganda small mammal populations were studied between April 1995 and March 1997 using the capture-mark-release-method and radio-telemetry. The 6 study plots were situated in the Imperata-Cymbopogon-grassland and in the bushland-grassland-mosaic and differed mainly in vegetation, habitat structures, cover and grazing pressure due to big game. The effect of fire was an important aspect to all questions of the study. In total 5.702 catches including 1.295 individuals out of 20 species of the families Muridae (12), Myoxidae (1) und Soricidae (7) were recorded in 65 trapping sessions. The most abundant species were Lemniscomys striatus, Mastomys natalensis and Arvicanthis nairobae. For all plots zoocoenosis and dominance structures are described as well as similarity of fauna and species diversity are compared. The population structures of the 3 most common species are compared in 2 plots of their highest abundance. Emphasis of the investigation is laid on the population development, sex ratio, weight and reproduction. Beyond the survival and turnover rates are determined for these populations. For all species habitat preferences are described. The range lenghts of L. striatus and M. natalensis were ascertained for different plots. Their dependence of population density, sex, sexual activity, body weight, rainfall and bush fire is revised. In all 9 L. striatus, 7 M. natalensis and 8 A. nairobae were radio-tracked successfully and their home range sizes, utilization patterns and activities investigated. For these species an inverse relationship between home range size and population density exists.',\n", + " 'inLanguage': 'en',\n", + " 'additionalType': 'HumanObservation',\n", + " 'dateCreated': '1999-10-19',\n", + " 'dateModified': '2018-01-22',\n", + " 'datePublished': '2018-01-22',\n", + " 'distribution': None,\n", + " 'isAccessibleForFree': {'@xsi:type': 'xs:boolean', '#text': 'true'},\n", + " 'size': {'@type': 'QuantitativeValue',\n", + " 'value': {'@xsi:type': 'xs:int', '#text': '267'},\n", + " 'unitText': 'records'},\n", + " 'license': {'@type': 'CreativeWork',\n", + " 'name': 'CC BY 4.0',\n", + " 'description': None},\n", + " 'spatialCoverage': {'@type': 'Country', 'name': 'Uganda', 'identifier': 'UG'},\n", + " 'temporalCoverage': '1995-06-13/1997-03-13',\n", + " 'reverse': {'citation': [{'@type': 'CreativeWork',\n", + " 'name': 'Publication 1 citing this record',\n", + " 'description': 'Aristida adscensionis cited from Hoffmann',\n", + " 'identifier': 'https://data-rebind.bgbm.org/gfbio/biocase/pub1'},\n", + " {'@type': 'CreativeWork',\n", + " 'name': 'Publication 2 citing this record',\n", + " 'description': 'Aristida adscensionis cited from Hoffmann',\n", + " 'identifier': 'https://data-rebind.bgbm.org/gfbio/biocase/pub2'},\n", + " {'@type': 'CreativeWork',\n", + " 'name': 'Publication 1 citing this record',\n", + " 'description': 'Bothriochloa insculpta cited from Hoffmann',\n", + " 'identifier': 'https://data-rebind.bgbm.org/gfbio/biocase/pub1'},\n", + " {'@type': 'CreativeWork',\n", + " 'name': 'Publication 2 citing this record',\n", + " 'description': 'Bothriochloa insculpta cited from Hoffmann',\n", + " 'identifier': 'https://data-rebind.bgbm.org/gfbio/biocase/pub2'}]},\n", + " 'about': [{'@type': 'Taxon',\n", + " 'name': 'Aristida adscensionis',\n", + " 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Bothriochloa insculpta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cenchrus ciliaris', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Chloris gayana', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Sporobolus pyramidalis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Themeda triandra', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Sida ovata', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Acacia hockii', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Achyranthes aspera', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Capparis tomentosa', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Erythrococca bongensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Euphorbia candelabrum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Flueggea virosa', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hoslundia opposita', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Ocimum suave', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Abutilon guineense', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Grewia similis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cissus quadrangularis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hyperthelia dissoluta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hyparrhenia rufa', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Abutilon hirtum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Lantana camara', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Euphorbia hirta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon',\n", + " 'name': 'Indigofera simplicifolia',\n", + " 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Indigofera spicata', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Tephrosia nana', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Vigna ambacensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Lantana trifolia', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Solanum incanum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Conyza stricta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Panicum maximum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Turraea robusta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Acacia sieberiana', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Tarenna graveolens', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cissus ovata', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Brachiaria eminii', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Indigofera arrecta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Leonotis nepetifolia', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Leucas martinicensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hibiscus aethiopicus', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cissus rotundifolia', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Heteropogon contortus', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cayratia ibuensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Maerua triphylla', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hibiscus aponeurus', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Piper sp.', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Pavetta albertina', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Plantae', 'taxonRank': 'regnum'},\n", + " {'@type': 'Taxon', 'name': 'Gramineae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Malvaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Mimosaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Amaranthaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Capparidaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Euphorbiaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Labiatae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Tiliaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Vitaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Verbenaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Papilioniaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Solanaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Compositae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Meliaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Rubiaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Piperaceae', 'taxonRank': 'familia'},\n", + " {'@type': 'Taxon', 'name': 'Aristida adscensionis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Bothriochloa insculpta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cenchrus ciliaris', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Chloris gayana', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Sporobolus pyramidalis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Themeda triandra', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Sida ovata', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Acacia hockii', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Achyranthes aspera', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Capparis tomentosa', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Erythrococca bongensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Euphorbia candelabrum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Flueggea virosa', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hoslundia opposita', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Ocimum suave', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Abutilon guineense', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Grewia similis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cissus quadrangularis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hyperthelia dissoluta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hyparrhenia rufa', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Abutilon hirtum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Lantana camara', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Euphorbia hirta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon',\n", + " 'name': 'Indigofera simplicifolia',\n", + " 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Indigofera spicata', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Tephrosia nana', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Vigna ambacensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Lantana trifolia', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Solanum incanum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Conyza stricta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Panicum maximum', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Turraea robusta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Acacia sieberiana', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Tarenna graveolens', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cissus ovata', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Brachiaria eminii', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Indigofera arrecta', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Leonotis nepetifolia', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Leucas martinicensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hibiscus aethiopicus', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cissus rotundifolia', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Heteropogon contortus', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Cayratia ibuensis', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Maerua triphylla', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Hibiscus aponeurus', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Piper sp.', 'taxonRank': 'Species'},\n", + " {'@type': 'Taxon', 'name': 'Pavetta albertina', 'taxonRank': 'Species'}],\n", + " 'publisher': {'@type': 'Organization',\n", + " 'name': 'GFBio Data Center BGBM',\n", + " 'email': 'gfbio@bgbm.org',\n", + " 'address': 'Königin-Luise-Str.6-8, 14195 Berlin, Germany'},\n", + " 'maintainer': {'@type': 'Organization',\n", + " 'name': 'GFBio Data Center BGBM',\n", + " 'email': 'gfbio@bgbm.org',\n", + " 'address': 'Königin-Luise-Str.6-8, 14195 Berlin, Germany'},\n", + " 'contributor': {'@type': 'Person',\n", + " 'name': 'Tom Friday Baluku, Maren Gleisberg'}}" ] }, - "execution_count": 51, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -522,9 +308,32 @@ "source": [ "#transform XML structure to Python dictionary structure\n", "schema_dict = xmltodict.parse(schema_xml)\n", + "schema_dict['jsonld']['@reverse'] = schema_dict['jsonld'].pop('reverse')\n", "schema_dict['jsonld']" ] }, + { + "cell_type": "code", + "execution_count": 6, + "id": "afe776d6", + "metadata": {}, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 's' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[6], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43ms\u001b[49m\n", + "\u001b[1;31mNameError\u001b[0m: name 's' is not defined" + ] + } + ], + "source": [ + "s" + ] + }, { "cell_type": "code", "execution_count": null, @@ -532,15 +341,70 @@ "metadata": {}, "outputs": [], "source": [ - "#TODO: aggregate taxon names to higher level here \n" + "# TODO: aggregate taxon names to higher level here\n", + "# get about list\n", + "import pygbif.species as species\n", + "schema_dict = xmltodict.parse(schema_xml)\n", + "about_list = schema_dict['jsonld']['about'].copy()\n", + "# for each entry request taxon information from GBIF and add to dict as taxonInfo\n", + "for about in about_list[:5]:\n", + " taxon = species.name_backbone(name=about['name'])\n", + " print(taxon)\n", + " about['taxonInfo'] = taxon\n", + "\n", + "about_list" ] }, { "cell_type": "code", - "execution_count": 52, - "id": "20b3effb", + "execution_count": null, + "id": "648671ee", "metadata": {}, "outputs": [], + "source": [ + "schema_dict['jsonld']['about']" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "dcb9feb6", + "metadata": {}, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 'about_list' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[2], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43mabout_list\u001b[49m\n", + "\u001b[1;31mNameError\u001b[0m: name 'about_list' is not defined" + ] + } + ], + "source": [ + "about_list" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "20b3effb", + "metadata": {}, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 'schema_dict' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[3], line 4\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[38;5;66;03m#convert data values\u001b[39;00m\n\u001b[0;32m 2\u001b[0m \u001b[38;5;66;03m#TODO: write algorithm to do that generically\u001b[39;00m\n\u001b[0;32m 3\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m----> 4\u001b[0m schema_dict[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mjsonld\u001b[39m\u001b[38;5;124m'\u001b[39m][\u001b[38;5;124m'\u001b[39m\u001b[38;5;124misAccessibleForFree\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mbool\u001b[39m(\u001b[43mschema_dict\u001b[49m[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mjsonld\u001b[39m\u001b[38;5;124m'\u001b[39m][\u001b[38;5;124m'\u001b[39m\u001b[38;5;124misAccessibleForFree\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[0;32m 5\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[0;32m 6\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n", + "\u001b[1;31mNameError\u001b[0m: name 'schema_dict' is not defined" + ] + } + ], "source": [ "#convert data values\n", "#TODO: write algorithm to do that generically\n", @@ -605,7 +469,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.9.4" } }, "nbformat": 4, diff --git a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml index a978265..3fe0b42 100644 --- a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml +++ b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml @@ -101,6 +101,18 @@ UG + + + Publication 1 citing this record + Aristida adscensionis cited from Hoffmann + https://data-rebind.bgbm.org/gfbio/biocase/pub1 + + + Publication 2 citing this record + Aristida adscensionis cited from Hoffmann + https://data-rebind.bgbm.org/gfbio/biocase/pub2 + + @@ -167,6 +179,18 @@ UG + + + Publication 1 citing this record + Bothriochloa insculpta cited from Hoffmann + https://data-rebind.bgbm.org/gfbio/biocase/pub3 + + + Publication 2 citing this record + Bothriochloa insculpta cited from Hoffmann + https://data-rebind.bgbm.org/gfbio/biocase/pub4 + + https://data-rebind.bgbm.org/gfbio/biocase/page/B/HoffmannPlants/4