Grays_part1 | | Embryology | 1.44 K | | okubo | 2023-11-30 | Testing | |
Gene_Chemical | | EMU abstract annotation | 0 | | zhoukaiyin | 2023-11-29 | Developing | |
bionlp-st-2016-SeeDev-dev | | Entities and event annotations from the development set of the BioNLP-ST 2016 SeeDev task.
SeeDev task focuses on seed storage and reserve accumulation on the model organism, Arabidopsis thaliana. The SeeDev task is based on the knowledge model Gene Regulation Network for Arabidopsis (GRNA) that meets the needs of text-mining (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse in other plant systems. It is also expected to meet the requirements of the integration of the text knowledge with knowledge derived from experimental data in view of modeling in systems biology.
GRNA model defines 16 different types of entities, and 22 types of event (in five sets of event types) that may be combined in complex events.
For more information, please refer to the task website
All annotations :
Train set
Development set
Test set (without events)
| 61 | | EstelleChaix | 2023-11-29 | Released | |
bionlp-st-2016-SeeDev-training | | Entities and event annotations from the training set of the BioNLP-ST 2016 SeeDev task.
SeeDev task focuses on seed storage and reserve accumulation on the model organism, Arabidopsis thaliana. The SeeDev task is based on the knowledge model Gene Regulation Network for Arabidopsis (GRNA) that meets the needs of text-mining (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse in other plant systems. It is also expected to meet the requirements of the integration of the text knowledge with knowledge derived from experimental data in view of modeling in systems biology.
GRNA model defines 16 different types of entities, and 22 types of event (in five sets of event types) that may be combined in complex events.
For more information, please refer to the task website
All annotations :
Train set
Development set
Test set (without events)
| 35 | | EstelleChaix | 2023-11-28 | Released | |
bionlp-st-2016-SeeDev-test | | Entities annotations from the test set of the BioNLP-ST 2016 SeeDev task.
SeeDev task focuses on seed storage and reserve accumulation on the model organism, Arabidopsis thaliana. The SeeDev task is based on the knowledge model Gene Regulation Network for Arabidopsis (GRNA) that meets the needs of text-mining (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse in other plant systems. It is also expected to meet the requirements of the integration of the text knowledge with knowledge derived from experimental data in view of modeling in systems biology.
GRNA model defines 16 different types of entities, and 22 types of event (in five sets of event types) that may be combined in complex events.
For more information, please refer to the task website
All annotations :
Train set
Development set
Test set (without events)
| 184 | | EstelleChaix | 2023-11-29 | Released | |
FirstAuthor10 | | FirstAuthor10 | 4.78 K | | AikoHIRAKI | 2023-11-29 | Developing | |
FA_PR25 | | FirstAuthor Protein Ontology 25 entries | 512 | | AikoHIRAKI | 2023-11-29 | Developing | |
FA_Top107-forWeb | | ※※※ !要データ加工! webリンク用には、この結果を加工して使っています。その他で使われる場合に、末尾記載の問題を別途解決する必要があります。 !要データ加工! ※※※
Top100+本来Top100に入るべきだった7レビューの計、107レビュー中99レビュー。
5414, 6076, 6930, 8403, 9643, 12112, 18544, 18829は、0denotationでドキュメント自体登録していません。
@AikoHIRAKIはtypoを修正したレビューフォルダ。
attributesの詳細はconfig参照。
※※※ !注意!
webリンク側のしばりで、選択文字列は複数のUniProtIDに対応していません。(例)Protein1~Protein7とある場合、
Protein1, 2, 3, 4, 5, 6, 7をさし、かつ全てにUniProtIDがあったとしても、1と7のみUniProtIDをとってきています。
"~"は、Protein2, 3, 4, 5, 6を意味していますが、positionではなく文字列で検索をかけているのと、見せ方の仕様上、これらのIDは全て未取得となっています。⇔GeneProteinでは"~"に2-6のIDsをもたせていました。
該当レビュー;14898(~=MAPK2, MAPK3, MAPK4, MAPK5, MAPK6), 10471(~=Ago2, Ago3)
---------------------------------------
(例)ProteinAB...ProteinCD...ProteinB...ProteinDとある場合、
ProteinABは、ProteinAとBというLexical_Cueになっています。ProteinCDも同様に、ProteinCとD。BとDだけでは、このレビュー内ではProteinBやProteinDをさすことが分かるのですが、それ以外で使用する場合に、BとDにそれぞれ該当UniProtIDをあてるのは不適切です。
該当レビュー;11957(β4=itgb4, β1=itgb1, β5=itgb5, β3=itgb3)
他の例が出てきたら順次、ここに記載していきます。当座、これらは削除する必要があります。
attributeで削除フラグをつけるか、Jakeの機能がTextAEに実装されれば解決するか、検討して、何かしら分かるようにしておきます。
(例)ProteinA/B とある場合、
webリンクでは、"ProteinA"にUniProtID-Aを、"/B"にUniProtID-Bをつけています(リンク側のしばり)。webリンク以外で使われる場合には、別プロジェクトのFA_Top100Plus-GeneProteinで行っていたようなRelationを使って、"/B"ではなく、"ProteinB"として、UniProtID-Bと対応させる必要があります。現状のとり方ですと、要Relation箇所は救済出来ません。
Lexical cueには"/B"とありますが、Objectには"ProteinB"と残してあるので、Objectを参照して下さい。
但し、言語処理のようなpositionがご入用な場合には上では対応出来ていません。
該当レビュー;11935(/4=BMP4), 14898(/2=LATS2), 7412(/2=TSC2), 4629(/2=CtBP2)
(webリンクでは、レビュー毎に完結しているので、"/B"がそのレビューで他の意味をなしていなければ対応出来るのと、文字列合致でリンクを貼っているためです。)
!注意! ※※※
RelationのmergedはTextAEの既存機能で既に出来ます。 | 10.3 K | | AikoHIRAKI | 2023-11-29 | Beta | |
cancer_precision | | for gene mutaiton and cancer therapy | 8 | | serenity | 2023-11-29 | Testing | |
FirstAuthor_s_Plants | | For only Plants | 4.3 K | | AikoHIRAKI | 2023-11-29 | Testing | |
SMAFIRA-Case-Studies-19735549 | | From: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv | 0 | | zebet | 2023-11-30 | Developing | |
SMAFIRA-Case-Studies-21494637 | | From: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv | 0 | | zebet | 2023-11-26 | Developing | |
SMAFIRA-Case-Studies-24204323 | | From: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv | 0 | | zebet | 2023-11-29 | Developing | |
SMAFIRA-Case-Studies-16850029 | | From: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv | 0 | | zebet | 2023-11-30 | Developing | |
Genomics_Informatics | | Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization.
Text corpus for this journal annotated with various levels of linguistic information would be a valuable resource as the process of information extraction requires syntactic, semantic, and higher levels of natural language processing. In this study, we publish our new corpus called GNI Corpus version 1.0, extracted and annotated from full texts of Genomics & Informatics, with NLTK (Natural Language ToolKit)-based text mining script. The preliminary version of the corpus could be used as a training and testing set of a system that serves a variety of functions for future biomedical text mining. | 35.3 K | Hyun-Seok Park | ewha-bio | 2023-11-29 | Beta | |
Glycan-Abbreviation | | Glycan-Abbreviation - GlycoNAVI Project | 0 | | ISSAKU YAMADA | 2023-11-29 | Testing | |
glycoprotein | | glycoprotein annotation | 54 | issaku yamada | ISSAKU YAMADA | 2023-11-29 | Testing | |
PathNERGold | | Gold standard used for training PathNER | 0 | Chengkin Wu | nikolamilosevic | 2023-11-29 | Developing | |
hahm_test | | hahm_test | 0 | hahm | kaist_nlp | 2019-04-02 | Testing | |
CORD-19_HIRAKI | | HIRAKI Annotation for CORD-19 | 2.98 K | | AikoHIRAKI | 2023-11-29 | Testing | |