WEKO3
アイテム
{"_buckets": {"deposit": "6ad634cb-b886-44a9-b46a-3c5bf36db920"}, "_deposit": {"created_by": 3, "id": "6058", "owners": [3], "pid": {"revision_id": 0, "type": "depid", "value": "6058"}, "status": "published"}, "_oai": {"id": "oai:kyutech.repo.nii.ac.jp:00006058", "sets": ["9"]}, "author_link": ["24857", "24859", "24877"], "item_21_biblio_info_6": {"attribute_name": "書誌情報", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2019-06-13", "bibliographicIssueDateType": "Issued"}, "bibliographicPageEnd": "329-14", "bibliographicPageStart": "329-1", "bibliographicVolumeNumber": "20", "bibliographic_titles": [{"bibliographic_title": "BMC Bioinformatics"}]}]}, "item_21_description_4": {"attribute_name": "抄録", "attribute_value_mlt": [{"subitem_description": "Background Co-occurrence networks—ecological associations between sampled populations of microbial communities inferred from taxonomic composition data obtained from high-throughput sequencing techniques—are widely used in microbial ecology. Several co-occurrence network methods have been proposed. Co-occurrence network methods only infer ecological associations and are often used to discuss species interactions. However, validity of this application of co-occurrence network methods is currently debated. In particular, they simply evaluate using parametric statistical models, even though microbial compositions are determined through population dynamics. Results We comprehensively evaluated the validity of common methods for inferring microbial ecological networks through realistic simulations. We evaluated how correctly nine widely used methods describe interaction patterns in ecological communities. Contrary to previous studies, the performance of the co-occurrence network methods on compositional data was almost equal to or less than that of classical methods (e.g., Pearson’s correlation). The methods described the interaction patterns in dense and/or heterogeneous networks rather inadequately. Co-occurrence network performance also depended upon interaction types; specifically, the interaction patterns in competitive communities were relatively accurately predicted while those in predator–prey (parasitic) communities were relatively inadequately predicted. Conclusions Our findings indicated that co-occurrence network approaches may be insufficient in interpreting species interactions in microbiome studies. However, the results do not diminish the importance of these approaches. Rather, they highlight the need for further careful evaluation of the validity of these much-used methods and the development of more suitable methods for inferring microbial ecological networks.", "subitem_description_type": "Abstract"}]}, "item_21_description_60": {"attribute_name": "資源タイプ", "attribute_value_mlt": [{"subitem_description": "Journal Article", "subitem_description_type": "Other"}]}, "item_21_full_name_3": {"attribute_name": "著者別名", "attribute_value_mlt": [{"nameIdentifiers": [{"nameIdentifier": "24859", "nameIdentifierScheme": "WEKO"}], "names": [{"name": "Hirano, H"}]}, {"affiliations": [{"affiliationNames": [{"affiliationName": "", "lang": "ja"}], "nameIdentifiers": []}], "familyNames": [{"familyName": "Takemoto", "familyNameLang": "en"}, {"familyName": "竹本", "familyNameLang": "ja"}, {"familyName": "タケモト", "familyNameLang": "ja-Kana"}], "givenNames": [{"givenName": "Kazuhiro", "givenNameLang": "en"}, {"givenName": "和広", "givenNameLang": "ja"}, {"givenName": "カズヒロ", "givenNameLang": "ja-Kana"}], "nameIdentifiers": [{"nameIdentifier": "24877", "nameIdentifierScheme": "WEKO"}, {"nameIdentifier": "40512356", "nameIdentifierScheme": "e-Rad", "nameIdentifierURI": "https://nrid.nii.ac.jp/ja/nrid/1000040512356"}, {"nameIdentifier": "35270356700 ", "nameIdentifierScheme": "Scopus著者ID", "nameIdentifierURI": "https://www.scopus.com/authid/detail.uri?authorId=35270356700 "}, {"nameIdentifier": "0000-0002-6355-1366", "nameIdentifierScheme": "ORCiD", "nameIdentifierURI": "https://orcid.org/0000-0002-6355-1366"}, {"nameIdentifier": "100000509", "nameIdentifierScheme": "九工大研究者情報", "nameIdentifierURI": "https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html"}], "names": [{"name": "Takemoto, Kazuhiro", "nameLang": "en"}, {"name": "竹本, 和広", "nameLang": "ja"}, {"name": "タケモト, カズヒロ", "nameLang": "ja-Kana"}]}]}, "item_21_link_62": {"attribute_name": "研究者情報", "attribute_value_mlt": [{"subitem_link_text": "https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html", "subitem_link_url": "https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html"}]}, "item_21_publisher_7": {"attribute_name": "出版者", "attribute_value_mlt": [{"subitem_publisher": "Biomed Central"}]}, "item_21_relation_12": {"attribute_name": "DOI", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:doi/10.1186/s12859-019-2915-1", "subitem_relation_type_select": "DOI"}}]}, "item_21_relation_14": {"attribute_name": "情報源", "attribute_value_mlt": [{"subitem_relation_name": [{"subitem_relation_name_text": "https://doi.org/10.1186/s12859-019-2915-1"}], "subitem_relation_type_id": {"subitem_relation_type_id_text": "https://doi.org/10.1186/s12859-019-2915-1", "subitem_relation_type_select": "DOI"}}]}, "item_21_rights_13": {"attribute_name": "権利", "attribute_value_mlt": [{"subitem_rights": "Copyright (c) The Author(s). 2019"}, {"subitem_rights": "Creative Commons Attribution 4.0 International License"}, {"subitem_rights": "http://creativecommons.org/licenses/by/4.0/"}]}, "item_21_select_59": {"attribute_name": "査読の有無", "attribute_value_mlt": [{"subitem_select_item": "yes"}]}, "item_21_source_id_8": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "1471-2105", "subitem_source_identifier_type": "ISSN"}]}, "item_21_subject_16": {"attribute_name": "日本十進分類法", "attribute_value_mlt": [{"subitem_subject": "465", "subitem_subject_scheme": "NDC"}]}, "item_21_text_28": {"attribute_name": "論文ID(連携)", "attribute_value_mlt": [{"subitem_text_value": "10342784"}]}, "item_21_text_36": {"attribute_name": "著者所属", "attribute_value_mlt": [{"subitem_text_value": "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan"}, {"subitem_text_value": "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan"}]}, "item_21_text_63": {"attribute_name": "連携ID", "attribute_value_mlt": [{"subitem_text_value": "7787"}]}, "item_21_version_type_58": {"attribute_name": "著者版フラグ", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_970fb48d4fbd8a85", "subitem_version_type": "VoR"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Hirano, Hokuto"}], "nameIdentifiers": [{"nameIdentifier": "24857", "nameIdentifierScheme": "WEKO"}]}, {"creatorAffiliations": [{"affiliationNameIdentifiers": [], "affiliationNames": [{"affiliationName": "", "affiliationNameLang": "ja"}]}], "creatorNames": [{"creatorName": "Takemoto, Kazuhiro", "creatorNameLang": "en"}, {"creatorName": "竹本, 和広", "creatorNameLang": "ja"}, {"creatorName": "タケモト, カズヒロ", "creatorNameLang": "ja-Kana"}], "familyNames": [{"familyName": "Takemoto", "familyNameLang": "en"}, {"familyName": "竹本", "familyNameLang": "ja"}, {"familyName": "タケモト", "familyNameLang": "ja-Kana"}], "givenNames": [{"givenName": "Kazuhiro", "givenNameLang": "en"}, {"givenName": "和広", "givenNameLang": "ja"}, {"givenName": "カズヒロ", "givenNameLang": "ja-Kana"}], "nameIdentifiers": [{"nameIdentifier": "24877", "nameIdentifierScheme": "WEKO"}, {"nameIdentifier": "40512356", "nameIdentifierScheme": "e-Rad", "nameIdentifierURI": "https://nrid.nii.ac.jp/ja/nrid/1000040512356"}, {"nameIdentifier": "35270356700 ", "nameIdentifierScheme": "Scopus著者ID", "nameIdentifierURI": "https://www.scopus.com/authid/detail.uri?authorId=35270356700 "}, {"nameIdentifier": "0000-0002-6355-1366", "nameIdentifierScheme": "ORCiD", "nameIdentifierURI": "https://orcid.org/0000-0002-6355-1366"}, {"nameIdentifier": "100000509", "nameIdentifierScheme": "九工大研究者情報", "nameIdentifierURI": "https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html"}]}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2019-07-02"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "s12859-019-2915-1.pdf", "filesize": [{"value": "1.4 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_free", "mimetype": "application/pdf", "size": 1400000.0, "url": {"label": "s12859-019-2915-1.pdf", "url": "https://kyutech.repo.nii.ac.jp/record/6058/files/s12859-019-2915-1.pdf"}, "version_id": "5f7be924-f8f6-4f5b-b526-a9de05bd4611"}]}, "item_keyword": {"attribute_name": "キーワード", "attribute_value_mlt": [{"subitem_subject": "Microbiome", "subitem_subject_scheme": "Other"}, {"subitem_subject": "Correlation network analysis", "subitem_subject_scheme": "Other"}, {"subitem_subject": "Microbial ecology", "subitem_subject_scheme": "Other"}, {"subitem_subject": "Complex networks", "subitem_subject_scheme": "Other"}]}, "item_language": {"attribute_name": "言語", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "資源タイプ", "attribute_value_mlt": [{"resourcetype": "journal article", "resourceuri": "http://purl.org/coar/resource_type/c_6501"}]}, "item_title": "Difficulty in inferring microbial community structure based on co-occurrence network approaches", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Difficulty in inferring microbial community structure based on co-occurrence network approaches"}]}, "item_type_id": "21", "owner": "3", "path": ["9"], "permalink_uri": "http://hdl.handle.net/10228/00007268", "pubdate": {"attribute_name": "公開日", "attribute_value": "2019-07-02"}, "publish_date": "2019-07-02", "publish_status": "0", "recid": "6058", "relation": {}, "relation_version_is_last": true, "title": ["Difficulty in inferring microbial community structure based on co-occurrence network approaches"], "weko_shared_id": 3}
Difficulty in inferring microbial community structure based on co-occurrence network approaches
http://hdl.handle.net/10228/00007268
http://hdl.handle.net/10228/00007268a293f83d-f2fe-42bb-bb69-27e3df717610
名前 / ファイル | ライセンス | アクション |
---|---|---|
s12859-019-2915-1.pdf (1.4 MB)
|
|
Item type | 学術雑誌論文 = Journal Article(1) | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
公開日 | 2019-07-02 | |||||||||||
資源タイプ | ||||||||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||||||||
資源タイプ | journal article | |||||||||||
タイトル | ||||||||||||
タイトル | Difficulty in inferring microbial community structure based on co-occurrence network approaches | |||||||||||
言語 | ||||||||||||
言語 | eng | |||||||||||
著者 |
Hirano, Hokuto
× Hirano, Hokuto× 竹本, 和広
WEKO
24877
|
|||||||||||
抄録 | ||||||||||||
内容記述タイプ | Abstract | |||||||||||
内容記述 | Background Co-occurrence networks—ecological associations between sampled populations of microbial communities inferred from taxonomic composition data obtained from high-throughput sequencing techniques—are widely used in microbial ecology. Several co-occurrence network methods have been proposed. Co-occurrence network methods only infer ecological associations and are often used to discuss species interactions. However, validity of this application of co-occurrence network methods is currently debated. In particular, they simply evaluate using parametric statistical models, even though microbial compositions are determined through population dynamics. Results We comprehensively evaluated the validity of common methods for inferring microbial ecological networks through realistic simulations. We evaluated how correctly nine widely used methods describe interaction patterns in ecological communities. Contrary to previous studies, the performance of the co-occurrence network methods on compositional data was almost equal to or less than that of classical methods (e.g., Pearson’s correlation). The methods described the interaction patterns in dense and/or heterogeneous networks rather inadequately. Co-occurrence network performance also depended upon interaction types; specifically, the interaction patterns in competitive communities were relatively accurately predicted while those in predator–prey (parasitic) communities were relatively inadequately predicted. Conclusions Our findings indicated that co-occurrence network approaches may be insufficient in interpreting species interactions in microbiome studies. However, the results do not diminish the importance of these approaches. Rather, they highlight the need for further careful evaluation of the validity of these much-used methods and the development of more suitable methods for inferring microbial ecological networks. | |||||||||||
書誌情報 |
BMC Bioinformatics 巻 20, p. 329-1-329-14, 発行日 2019-06-13 |
|||||||||||
出版社 | ||||||||||||
出版者 | Biomed Central | |||||||||||
DOI | ||||||||||||
関連タイプ | isIdenticalTo | |||||||||||
識別子タイプ | DOI | |||||||||||
関連識別子 | info:doi/10.1186/s12859-019-2915-1 | |||||||||||
日本十進分類法 | ||||||||||||
主題Scheme | NDC | |||||||||||
主題 | 465 | |||||||||||
ISSN | ||||||||||||
収録物識別子タイプ | ISSN | |||||||||||
収録物識別子 | 1471-2105 | |||||||||||
著作権関連情報 | ||||||||||||
権利情報 | Copyright (c) The Author(s). 2019 | |||||||||||
著作権関連情報 | ||||||||||||
権利情報 | Creative Commons Attribution 4.0 International License | |||||||||||
著作権関連情報 | ||||||||||||
権利情報 | http://creativecommons.org/licenses/by/4.0/ | |||||||||||
キーワード | ||||||||||||
主題Scheme | Other | |||||||||||
主題 | Microbiome | |||||||||||
キーワード | ||||||||||||
主題Scheme | Other | |||||||||||
主題 | Correlation network analysis | |||||||||||
キーワード | ||||||||||||
主題Scheme | Other | |||||||||||
主題 | Microbial ecology | |||||||||||
キーワード | ||||||||||||
主題Scheme | Other | |||||||||||
主題 | Complex networks | |||||||||||
出版タイプ | ||||||||||||
出版タイプ | VoR | |||||||||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||||||||
査読の有無 | ||||||||||||
値 | yes | |||||||||||
研究者情報 | ||||||||||||
https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html | ||||||||||||
論文ID(連携) | ||||||||||||
10342784 | ||||||||||||
連携ID | ||||||||||||
7787 | ||||||||||||
資料タイプ | ||||||||||||
内容記述タイプ | Other | |||||||||||
内容記述 | Journal Article | |||||||||||
著者別名 | ||||||||||||
姓名 | Hirano, H | |||||||||||
著者別名 | ||||||||||||
姓名 | Takemoto, Kazuhiro | |||||||||||
言語 | en | |||||||||||
姓名 | 竹本, 和広 | |||||||||||
言語 | ja | |||||||||||
姓名 | タケモト, カズヒロ | |||||||||||
言語 | ja-Kana | |||||||||||
著者所属 | ||||||||||||
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan | ||||||||||||
著者所属 | ||||||||||||
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan | ||||||||||||
情報源 | ||||||||||||
識別子タイプ | DOI | |||||||||||
関連識別子 | https://doi.org/10.1186/s12859-019-2915-1 | |||||||||||
関連名称 | https://doi.org/10.1186/s12859-019-2915-1 |