毎木調査データをDarwin Core Archiveで公開した話
伊東宏樹
2023-02-16
はじめに
※ この発表ファイルは
https://ito4303.github.io/DarwinCoreArchive.html
に置いてあります。
背景
- 苫小牧林冠破壊調査地（十文字プロット）
- 洞爺丸台風による林冠破壊後の森林更新を1957年からモニタリング
- 2016年調査
- この年までの調査結果をDarwin Core Archive形式にまとめて、データペーパーとしたものがEcological Researchに掲載された (Itô et al. 2018)
- 2022年調査
- データをアップデート
Darwin Core / Darwin Core Archive
Darwin Core
- 生物多様性情報を記述するデータフォーマット
- GBIF (Global Biodiversity Information Facility) などで採用されている
- もともとは標本データのため
- occurrence (出現, 存在) データ
- コンマやタブ区切りのテキストファイル（XMLやRDFもあり）
Darwin Core Archive
- 生物多様性データとメタデータを一体化（zipで単一ファイルに）
- コアデータ + メタデータ (+ 拡張データ)
- occurrence以外のデータも扱えるようにする
コアデータの形式 (3種類)
- Occurrence data
- 出現（存在）データ
- 個体単位
- Checklist data
- 地域チェックリスト（ファウナ, フロラ）
- Sampling-event data
- 生態学調査データ (☞ 大澤・戸津 2017)
- 1回の調査 (sampling-event) が単位
拡張形式（例）
- Darwin Core Measurement or Facts
- 測定データ
- Simple Multimedia
- 画像・動画・音声
- Literature References
- 文献情報
- などなど
苫小牧林冠破壊調査地のデータ
FileMaker Pro データベース
データ処理の流れ
Darwin Core Archiveの構造
メタデータ
- eml.xml
Ecological Metadata Language (EML) により記述されたメタデータ
- データの概要、ライセンス、連絡先など
- meta.xml
- データ構造の定義
メタデータの内容
<eml:eml xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:dc="http://purl.org/dc/terms/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 http://rs.gbif.org/schema/eml-gbif-profile/1.1/eml.xsd" packageId="doi:10.1007/s11284-018-1559-3/v2.0" system="http://gbif.org" scope="system" xml:lang="eng">
<dataset>
<title xml:lang="eng">
Long-term data on forest regeneration after catastrophic windthrow in Tomakomai, Hokkaido, northern Japan
</title>
<creator>
<individualName>
<givenName>Hiroki</givenName>
<surName>Itô</surName>
</individualName>
<organizationName>Forestry and Forest Products Research Institute</organizationName>
<positionName>Leader of the silviculture research group, Hokkaido Research Center</positionName>
<address>
<deliveryPoint>Hitsujigaoka 7</deliveryPoint>
<city>Sapporo</city>
<administrativeArea>Hokkaido</administrativeArea>
<postalCode>062-8516</postalCode>
<country>JP</country>
</address>
<electronicMailAddress>abies.firma@gmail.com</electronicMailAddress>
<userId directory="http://orcid.org/">0000-0003-2243-1007</userId>
</creator>
<metadataProvider>
<individualName>
<givenName>Hiroki</givenName>
<surName>Itô</surName>
</individualName>
<organizationName>Forestry and Forest Products Research Institute</organizationName>
<positionName>Leader of the silviculture research group, Hokkaido Research Center</positionName>
<address>
<deliveryPoint>Hitsujigaoka 7</deliveryPoint>
<city>Sapporo</city>
<administrativeArea>Hokkaido</administrativeArea>
<postalCode>062-8516</postalCode>
<country>JP</country>
</address>
<electronicMailAddress>abies.firma@gmail.com</electronicMailAddress>
<userId directory="http://orcid.org/">0000-0003-2243-1007</userId>
</metadataProvider>
<pubDate>2023-02-08</pubDate>
<language>eng</language>
<abstract>
<para>
Typhoon No. 15 in 1954 (Marie) caused catastrophic windthrow in Hokkaido, northern Japan. The Tomakomai District of the National Forest was one of the forests severely damaged. A study site was established in a stand of the National Forest within the jurisdiction of the Iburi East District Forest Office. The stand was located on the eastern slope of Mt. Tarumae at an elevation of approximately 300–310 m a.s.l. at an angle of approximately 5°. Two belts sized 4 m × 40 m, crossing at right angles at the center (total area: 304 m^2), were established within the site in 1957, and censuses on regeneration were conducted in 1957, 1970, 1973, 1978, 1983, 1990, 1996, 2001, 2006, 2011, 2016, and 2022. All stems of coniferous tree species (height ≥ 10 cm) that regenerated in the belts were marked. For broadleaved tree species, all stems with height ≥ 1.3 m were marked in 1957–1990, but stems with height ≥ 10 cm were marked after 1996. Height was measured for all marked stems, and the diameter at breast height was measured for stems with height ≥ 1.3 m. During the censuses, 27 coniferous and broadleaved tree species were identified and three more species were identified to the genus level. There are 3,431 records for the occurrence data and 12,558 records for the measurement data, including missing values.
</para>
</abstract>
<keywordSet>
<keyword>Occurrence</keyword>
<keywordThesaurus>
GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type.xml
</keywordThesaurus>
</keywordSet>
<intellectualRights>
<para>
This work is licensed under a
<ulink url="http://creativecommons.org/licenses/by/4.0/legalcode">
<citetitle>Creative Commons Attribution (CC-BY) 4.0 License</citetitle>
</ulink>
.
</para>
</intellectualRights>
<coverage>
<geographicCoverage>
<geographicDescription>Tomakomai, Hokkaido, Japan</geographicDescription>
<boundingCoordinates>
<westBoundingCoordinate>141.432</westBoundingCoordinate>
<eastBoundingCoordinate>141.432</eastBoundingCoordinate>
<northBoundingCoordinate>42.69</northBoundingCoordinate>
<southBoundingCoordinate>42.69</southBoundingCoordinate>
</boundingCoordinates>
</geographicCoverage>
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>1957</calendarDate>
</beginDate>
<endDate>
<calendarDate>2022</calendarDate>
</endDate>
</rangeOfDates>
</temporalCoverage>
</coverage>
<maintenance>
<description>
<para/>
</description>
<maintenanceUpdateFrequency>unkown</maintenanceUpdateFrequency>
</maintenance>
<contact>
<individualName>
<givenName>Hiroki</givenName>
<surName>Itô</surName>
</individualName>
<organizationName>Forestry and Forest Products Research Institute</organizationName>
<positionName>Leader of the silviculture research group, Hokkaido Research Center</positionName>
<address>
<deliveryPoint>Hitsujigaoka 7</deliveryPoint>
<city>Sapporo</city>
<administrativeArea>Hokkaido</administrativeArea>
<postalCode>062-8516</postalCode>
<country>JP</country>
</address>
<electronicMailAddress>abies.firma@gmail.com</electronicMailAddress>
<userId directory="http://orcid.org/">0000-0003-2243-1007</userId>
</contact>
<methods>
<methodStep>
<description>
<para/>
</description>
</methodStep>
</methods>
</dataset>
<additionalMetadata>
<metadata>
<gbif>
<dateStamp>2023-02-08T02:00:00+00:00</dateStamp>
<hierarchyLevel>dataset</hierarchyLevel>
</gbif>
</metadata>
</additionalMetadata>
</eml:eml><?xml version="1.0"?>
<archive xmlns="http://rs.tdwg.org/dwc/text/">
<core encoding="UTF-8" linesTerminatedBy="\n" fieldsTerminatedBy="\t" fieldsEnclosedBy="" ignoreHeaderLines="1" rowType="http://rs.tdwg.org/dwc/terms/Occurrence">
<files>
<location>Tomakomai1463_occ.txt</location>
</files>
<id index="0"/>
<field default="HumanObservation" term="http://rs.tdwg.org/dwc/terms/basisOfRecord"/>
<field default="2023-02-08T02:00:00Z" term="http://purl.org/dc/terms/modified"/>
<field default="Forestry and Forest Products Research Institute, Japan" term="http://purl.org/dc/terms/rightsHolder"/>
<field default="FFPRI" term="http://rs.tdwg.org/dwc/terms/institutionCode"/>
<field default="Tomakomai1463" term="http://rs.tdwg.org/dwc/terms/collectionCode"/>
<field default="Hokkaido" term="http://rs.tdwg.org/dwc/terms/island"/>
<field default="Japan" term="http://rs.tdwg.org/dwc/terms/country"/>
<field default="JP" term="http://rs.tdwg.org/dwc/terms/countryCode"/>
<field default="Hokkaido" term="http://rs.tdwg.org/dwc/terms/stateProvince"/>
<field default="Tomakomai" term="http://rs.tdwg.org/dwc/terms/municipality"/>
<field default="300" term="http://rs.tdwg.org/dwc/terms/minimumElevationInMeters"/>
<field default="310" term="http://rs.tdwg.org/dwc/terms/maximumElevationInMeters"/>
<field default="42.690269" term="http://rs.tdwg.org/dwc/terms/decimalLatitude"/>
<field default="141.432472" term="http://rs.tdwg.org/dwc/terms/decimalLongitude"/>
<field default="WGS84" term="http://rs.tdwg.org/dwc/terms/geodeticDatum"/>
<field default="20" term="http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters"/>
<field index="1" term="http://rs.tdwg.org/dwc/terms/catalogNumber"/>
<field index="2" term="http://rs.tdwg.org/dwc/terms/eventDate"/>
<field index="3" term="http://rs.tdwg.org/dwc/terms/scientificName"/>
<field index="4" term="http://rs.tdwg.org/dwc/terms/kingdom"/>
<field index="5" term="http://rs.tdwg.org/dwc/terms/phylum"/>
<field index="6" term="http://rs.tdwg.org/dwc/terms/class"/>
<field index="7" term="http://rs.tdwg.org/dwc/terms/order"/>
<field index="8" term="http://rs.tdwg.org/dwc/terms/family"/>
<field index="9" term="http://rs.tdwg.org/dwc/terms/genus"/>
<field index="10" term="http://rs.tdwg.org/dwc/terms/specificEpithet"/>
<field index="11" term="http://rs.tdwg.org/dwc/terms/infraspecificEpithet"/>
<field index="12" term="http://rs.tdwg.org/dwc/terms/taxonRank"/>
</core>
<extension encoding="UTF-8" linesTerminatedBy="\n" fieldsTerminatedBy="\t" fieldsEnclosedBy="" ignoreHeaderLines="1" rowType="http://rs.tdwg.org/dwc/terms/MeasurementOrFact">
<files>
<location>Tomakomai1463_mea.txt</location>
</files>
<coreid index="0"/>
<field index="1" term="http://rs.tdwg.org/dwc/terms/measurementID"/>
<field index="2" term="http://rs.tdwg.org/dwc/terms/measurementType"/>
<field index="3" term="http://rs.tdwg.org/dwc/terms/measurementValue"/>
<field index="4" term="http://rs.tdwg.org/dwc/terms/measurementAccuracy"/>
<field index="5" term="http://rs.tdwg.org/dwc/terms/measurementUnit"/>
<field index="6" term="http://rs.tdwg.org/dwc/terms/measurementDeterminedDate"/>
</extension>
</archive>データ
- Core: Occurrence data
- 個体（樹幹）を単位として測定しているので
- Extension: Measurement or Facts
- 樹高または胸高直径
データの内容
| occurrenceID | catalogNumber | eventDate | scientificName | kingdom | phylum | class | order | family | genus | specificEpithet | infraspecificEpithet | taxonRank |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| urn:catalog:FFPRI:Tomakomai1463:00001 | 1 | 2006-06-21/2011-09-21 | Fraxinus lanuginosa Koidz. f. serrata (Nakai) Murata | Plantae | Euphyllophytes | Magnoliopsida | Lamiales | Oleaceae | Fraxinus | lanuginosa | serrata | forma |
| urn:catalog:FFPRI:Tomakomai1463:00002 | 2 | 2006-06-20/2011-09-21 | Fraxinus lanuginosa Koidz. f. serrata (Nakai) Murata | Plantae | Euphyllophytes | Magnoliopsida | Lamiales | Oleaceae | Fraxinus | lanuginosa | serrata | forma |
| urn:catalog:FFPRI:Tomakomai1463:00003 | 3 | 2006-06-21/2011-09-21 | Fraxinus lanuginosa Koidz. f. serrata (Nakai) Murata | Plantae | Euphyllophytes | Magnoliopsida | Lamiales | Oleaceae | Fraxinus | lanuginosa | serrata | forma |
| urn:catalog:FFPRI:Tomakomai1463:00004 | 4 | 2006-06-21/2016-11-02 | Fraxinus lanuginosa Koidz. f. serrata (Nakai) Murata | Plantae | Euphyllophytes | Magnoliopsida | Lamiales | Oleaceae | Fraxinus | lanuginosa | serrata | forma |
| （中略） | ||||||||||||
| urn:catalog:FFPRI:Tomakomai1463:03510 | 3510 | 2022-10-26/2022-10-26 | Abies sachalinensis (F.Schmidt) Mast. | Plantae | Euphyllophytes | Pinopsida | Pinales | Pinaceae | Abies | sachalinensis | species | |
| urn:catalog:FFPRI:Tomakomai1463:03511 | 3511 | 2022-10-26/2022-10-26 | Abies sachalinensis (F.Schmidt) Mast. | Plantae | Euphyllophytes | Pinopsida | Pinales | Pinaceae | Abies | sachalinensis | species |
| CoreID | measurementID | measurementType | measurementValue | measurementAccuracy | measurementUnit | measurementDeterminedDate |
|---|---|---|---|---|---|---|
| urn:catalog:FFPRI:Tomakomai1463:00001 | 8556 | Height | 18 | 1 | cm | 2006-06-21 |
| urn:catalog:FFPRI:Tomakomai1463:00001 | 9116 | Height | 31 | 1 | cm | 2011-09-21 |
| （中略） | ||||||
| urn:catalog:FFPRI:Tomakomai1463:00333 | 1012 | Height | 130 | 1 | cm | 1970-07 |
| urn:catalog:FFPRI:Tomakomai1463:00333 | 1013 | Diameter at Breast Height | 0.5 | 0.1 | cm | 1970-07 |
| （中略） | ||||||
| urn:catalog:FFPRI:Tomakomai1463:03510 | 12571 | Height | 10 | 1 | cm | 2022-10-26 |
| urn:catalog:FFPRI:Tomakomai1463:03511 | 12572 | Height | 11 | 1 | cm | 2022-10-26 |
データの利用
Rからの利用
出現データと測定データをそれぞれ読み込んで、結合する。
必要なデータを抽出してグラフを作成する。
出現データの読み込み
# A tibble: 3,430 × 13
occurre…¹ catal…² event…³ scien…⁴ kingdom phylum class order family genus
<chr> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 urn:cata… 1 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
2 urn:cata… 2 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
3 urn:cata… 3 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
4 urn:cata… 4 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
5 urn:cata… 5 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
6 urn:cata… 6 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
7 urn:cata… 7 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
8 urn:cata… 8 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
9 urn:cata… 9 2001-1… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
10 urn:cata… 10 2006-0… Fraxin… Plantae Euphy… Magn… Lami… Oleac… Frax…
# … with 3,420 more rows, 3 more variables: specificEpithet <chr>,
# infraspecificEpithet <chr>, taxonRank <chr>, and abbreviated variable
# names ¹occurrenceID, ²catalogNumber, ³eventDate, ⁴scientificName測定データの読み込み
# A tibble: 12,558 × 7
CoreID measu…¹ measu…² measu…³ measu…⁴ measu…⁵ measu…⁶
<chr> <dbl> <chr> <dbl> <dbl> <chr> <chr>
1 urn:catalog:FFPRI:Tomako… 8556 Height 18 1 cm 2006-0…
2 urn:catalog:FFPRI:Tomako… 9116 Height 31 1 cm 2011-0…
3 urn:catalog:FFPRI:Tomako… 8557 Height 18 1 cm 2006-0…
4 urn:catalog:FFPRI:Tomako… 9117 Height 29 1 cm 2011-0…
5 urn:catalog:FFPRI:Tomako… 8558 Height 32 1 cm 2006-0…
6 urn:catalog:FFPRI:Tomako… 9118 Height 26 1 cm 2011-0…
7 urn:catalog:FFPRI:Tomako… 8559 Height 46 1 cm 2006-0…
8 urn:catalog:FFPRI:Tomako… 9119 Height 25 1 cm 2011-0…
9 urn:catalog:FFPRI:Tomako… 10195 Height 22 1 cm 2016-1…
10 urn:catalog:FFPRI:Tomako… 8560 Height 24 1 cm 2006-0…
# … with 12,548 more rows, and abbreviated variable names ¹measurementID,
# ²measurementType, ³measurementValue, ⁴measurementAccuracy,
# ⁵measurementUnit, ⁶measurementDeterminedDateデータの結合と整理
各樹幹について各年の樹高データを抽出する。
height_data <-
# 測定データに出現データを結合
dplyr::left_join(mea_data, occ_data,
by = c("CoreID" = "occurrenceID")) %>%
# 必要な項目を抽出
dplyr::transmute(catalogNumber,
Species = str_c(genus, " ", specificEpithet),
measurementType, measurementValue,
Year = str_sub(measurementDeterminedDate, 1, 4) %>%
as.integer()) %>%
# 不明種を除去し、樹高データを抽出
dplyr::filter(!is.na(Species),
measurementType == "Height") %>%
# 2016年データの一部は2017年に測定したので統合
dplyr::mutate(Year = if_else(Year == 2017L, 2016L, Year))# A tibble: 8,893 × 5
catalogNumber Species measurementType measurementValue Year
<dbl> <chr> <chr> <dbl> <int>
1 1 Fraxinus lanuginosa Height 18 2006
2 1 Fraxinus lanuginosa Height 31 2011
3 2 Fraxinus lanuginosa Height 18 2006
4 2 Fraxinus lanuginosa Height 29 2011
5 3 Fraxinus lanuginosa Height 32 2006
6 3 Fraxinus lanuginosa Height 26 2011
7 4 Fraxinus lanuginosa Height 46 2006
8 4 Fraxinus lanuginosa Height 25 2011
9 4 Fraxinus lanuginosa Height 22 2016
10 5 Fraxinus lanuginosa Height 24 2006
# … with 8,883 more rowsグラフ表示
エゾマツとトドマツの最大樹高をプロット
plot_max_height <- height_data %>%
# エゾマツとトドマツを抽出
dplyr::filter(Species %in% c("Picea jezoensis",
"Abies sachalinensis")) %>%
# 樹種と測定年でグループ化
dplyr::group_by(Species, Year) %>%
# 樹種・測定年ごとの最大樹高(m)を求める
dplyr::summarise(Max_height = max(measurementValue, na.rm = TRUE) / 100,
.groups = "drop") %>%
ggplot(aes(x = Year, y = Max_height, colour = Species)) +
geom_line(size = 2) +
ylim(0, NA) + labs(y = "Max height (m)") +
theme_grey(base_size = 14)
おわりに
- 生態学データ（毎木調査・個体数データなど）は、研究室での入力・保管フォーマットはさまざま
- Darwin Core Archiveとして出力することで、共通フォーマットとして利用可能
参考文献
- Itô et al. (2018) Ecological Research 33: 283–283. doi:10.1007/s11284-018-1559-3
- 大澤・戸津 (2017) 保全生態学研究 22:371–381 doi:10.18960/hozen.22.2_371