• Scikit-Multilearn
• geniass
• geniatagger
• MySQL
• Matlab

To be added later.

The database SQL file: synthetic_biology.sql. This database consists of the following tables: author, cited_author, cited_article_author, citing_article, citing_article_cited_article, citing_article_keyword, keyword, target_article, target_article_author, and target_article_keyword.

SELECT id, title, doi, pmid, pmc_id FROM target_article WHERE doi IS NULL; 

To export the above records to target_article_dois.xlsx in the directory data, and then correct manually them one by one.

Once correction is done, to run TargetArticleDoiUpdater.java to import the related information in the file data/target_article_dois.xlsx into MySQL database.

There are still three duplications with id = “WOS:000246296800029” and “WOS:000247372300026”, id = “WOS:000297670800005” and “WOS:000293697700003”, and id = “WOS:000393719000030” and id = “WOS:000394061000172”. To run the following sql, the duplications will be removed.

DELETE FROM target_article_author WHERE target_article_id = "WOS:000247372300026"; 
DELETE FROM target_article_keyword WHERE target_article_id = "WOS:000247372300026"; 
DELETE FROM target_article WHERE id = "WOS:000247372300026"; 
 
DELETE FROM target_article_author WHERE target_article_id = "WOS:000293697700003"; 
DELETE FROM target_article_keyword WHERE target_article_id = "WOS:000293697700003"; 
DELETE FROM target_article WHERE id = "WOS:000293697700003"; 
 
DELETE FROM target_article_author WHERE target_article_id = "WOS:000394061000172"; 
DELETE FROM target_article_keyword WHERE target_article_id = "WOS:000394061000172"; 
DELETE FROM target_article WHERE id = "WOS:000394061000172"; 

However, several target articles are attached wrong DOI names or have still no DOI names. To run the following sql, the resulting DOI names will be corrected or added.

UPDATE target_article SET doi = "10.2307/24102078" WHERE id = "WOS:000252249700032"; 
UPDATE target_article SET doi = "10.1007/978-3-540-77962-9_9" WHERE id = "WOS:000253797300009"; 
UPDATE target_article SET doi = "10.1007/978-3-540-68894-5_7" WHERE id = "WOS:000265422400007"; 
UPDATE target_article SET doi = "10.4028/WWW.SCIENTIFIC.NET/AST.58.10" WHERE id = "WOS:000266359100002"; 
UPDATE target_article SET doi = "10.1080/00365520310000654A" WHERE id = "WOS:000181977200013"; 
UPDATE target_article SET doi = "10.1016/J.JMB.2004.06.053" WHERE id = "WOS:000223379400019"; 
UPDATE target_article SET doi = "10.1145/2024724.2024750" WHERE id = "WOS:000297360000020"; 
UPDATE target_article SET doi = "10.5897/AJB11.1057" WHERE id = "WOS:000298540000011"; 
UPDATE target_article SET doi = "10.1515/1544-6115.1761" WHERE id = "WOS:000306831100007"; 
UPDATE target_article SET doi = "10.1097/00006231-200306000-00013" WHERE id = "WOS:000183373800013"; 
UPDATE target_article SET doi = "10.1097/00005176-200406001-00720" WHERE id = "WOS:000227354700101"; 

SELECT ta.id AS id, ta.title AS title, ta.doi AS doi, ta.pmid AS pmid, ta.pmc_id AS pmcid, ta_a.author_id AS author_id, a.full_name AS full_name, ta_a.seq_no AS seq_no, ta_a.is_reprint AS is_reprint FROM target_article AS ta, target_article_author AS ta_a, author AS a  WHERE ta.id = ta_a.target_article_id AND ta_a.author_id = a.id AND ta.id <= "WOS:000250809900012" ORDER BY id ASC;
 
SELECT ta.id AS id, ta.title AS title, ta.doi AS doi, ta.pmid AS pmid, ta.pmc_id AS pmcid, ta_a.author_id AS author_id, a.full_name AS full_name, ta_a.seq_no AS seq_no, ta_a.is_reprint AS is_reprint FROM target_article AS ta, target_article_author AS ta_a, author AS a  WHERE ta.id = ta_a.target_article_id AND ta_a.author_id = a.id AND ta.id > "WOS:000250809900012" AND ta.id <= "WOS:000286359100002" ORDER BY id ASC;
 
SELECT ta.id AS id, ta.title AS title, ta.doi AS doi, ta.pmid AS pmid, ta.pmc_id AS pmcid, ta_a.author_id AS author_id, a.full_name AS full_name, ta_a.seq_no AS seq_no, ta_a.is_reprint AS is_reprint FROM target_article AS ta, target_article_author AS ta_a, author AS a  WHERE ta.id = ta_a.target_article_id AND ta_a.author_id = a.id AND ta.id > "WOS:000286359100002" ORDER BY id ASC; 

To export the above records to synthetic_biology1.xlsx, synthetic_biology2.xlsx and synthetic_biology3.xlsx in the directory data, and then check manually them one by one.

Once correction is done, to run TargetArticleSeqNoAndIsReprintUpdater.java in the package cn.edu.bjut.ui.

For unknown reasons, three coauthors are missed from the publication with id = ““WOS:000365103600006””. To conduct the following sql statements to supplement them.

INSERT author (id, full_name, last_name, first_name) VALUES (10846, "Linard, Alban", "Linard", "Alban"); 
INSERT author (id, full_name, last_name, first_name) VALUES (10849, "Bóbeda, Edmundo López", "Bóbeda", "Edmundo López"); 
INSERT author (id, full_name, last_name, first_name) VALUES (10851, "Marechal, Alexis", "Marechal", "Alexis"); 
 
INSERT target_article_author (target_article_id, author_id, seq_no_original, seq_no, is_reprint_original, is_reprint) VALUES ("WOS:000365103600006", 10846, 4, 4, 0, 0); 
INSERT target_article_author (target_article_id, author_id, seq_no_original, seq_no, is_reprint_original, is_reprint) VALUES ("WOS:000365103600006", 10849, 5, 5, 0, 0); 
INSERT target_article_author (target_article_id, author_id, seq_no_original, seq_no, is_reprint_original, is_reprint) VALUES ("WOS:000365103600006", 10851, 6, 6, 0, 0); 

To run DownloadByWosId.java, a file citing_article.wos_id in the directory data will be generated. According to this file, to fetch full-record and cited references in the format of bibtex from Web of Science, and to save them in the directory data/wos/citing.

To run CitingArticleBibTexImporter.java.