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{"title"=>"On the Ontology Based Representation of Cell Lines", "type"=>"journal", "authors"=>[{"first_name"=>"Matthias", "last_name"=>"Ganzinger", "scopus_author_id"=>"18433968800"}, {"first_name"=>"Shan", "last_name"=>"He", "scopus_author_id"=>"55468021100"}, {"first_name"=>"Kai", "last_name"=>"Breuhahn", "scopus_author_id"=>"6603321273"}, {"first_name"=>"Petra", "last_name"=>"Knaup", "scopus_author_id"=>"6701560333"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84868694684", "sgr"=>"84868694684", "pui"=>"366024909", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "pmid"=>"23144907", "doi"=>"10.1371/journal.pone.0048584"}, "id"=>"ac1a198b-d4f5-34e2-a3ce-fef3061f0bf3", "abstract"=>"Cell lines are frequently used as highly standardized and reproducible in vitro models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT) integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.", "link"=>"http://www.mendeley.com/research/ontology-based-representation-cell-lines", "reader_count"=>18, "reader_count_by_academic_status"=>{"Researcher"=>5, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>4, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>5, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>4, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>2, "Philosophy"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>2, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Philosophy"=>{"Philosophy"=>1}}, "group_count"=>1}

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• http://doi.org/10.1016/j.jbi.2018.02.010

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• {"id"=>"268149751244025858", "text"=>"On the Ontology Based Representation of Cell Lines\nhttp://t.co/5rMCb6My", "created_at"=>"2012-11-13T00:34:17Z", "user"=>"maskot1977", "user_name"=>"Mas Kot", "user_profile_image"=>"http://a0.twimg.com/profile_images/405789674/06-09-14_16-26_normal.jpg"}
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• {"id"=>"268252067938832384", "text"=>"RT @maskot1977: On the Ontology Based Representation of Cell Lines\nhttp://t.co/5rMCb6My", "created_at"=>"2012-11-13T07:20:51Z", "user"=>"abhik1368", "user_name"=>"Abhik Seal", "user_profile_image"=>"http://a0.twimg.com/profile_images/1311363662/a2_normal.jpg"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/546893"], "description"=>"<p>The STR loci shown here are derived from the forensic STR system Combined DNA Index System (CODIS) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Budowle1\" target=\"_blank\">[31]</a>. Since the system is established to identify human cells with a high probability, it is also used by various cell banks for identifying human cell lines.</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "cell biology", "computer science", "developmental biology", "Non-clinical medicine"], "article_id"=>217380, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t005", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_STR_marker_used_in_CCONT_/217380", "title"=>"STR marker used in CCONT.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:03:00"}
• {"files"=>["https://ndownloader.figshare.com/files/546987"], "description"=>"<p>This table summarizes the evaluation techniques suggested by Obrst et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Obrst1\" target=\"_blank\">[16]</a> for use with ontologies in life sciences. The techniques one to three were applied when evaluating CCONT.</p>", "links"=>[], "tags"=>["techniques", "et"], "article_id"=>217479, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ontology_evaluation_techniques_Obrst_et_al_16_/217479", "title"=>"Ontology evaluation techniques (Obrst et al. [16]).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:04:39"}
• {"files"=>["https://ndownloader.figshare.com/files/546954"], "description"=>"<p>The same information is attributed to different data fields in the cell banks we reviewed. This table shows how the two sample terms ‘medium’ and ‘organ’ are handled in the respective databases. The fields marked by * are free text fields. They are also used for other types of data.</p>", "links"=>[], "tags"=>["fields"], "article_id"=>217448, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_data_fields_in_cell_bank_databases_/217448", "title"=>"Sample data fields in cell bank databases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:04:08"}
• {"files"=>["https://ndownloader.figshare.com/files/546827"], "description"=>"<p>In CCONT, we use the relationships inherited from EFO <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Malone1\" target=\"_blank\">[21]</a>. In this table we show the labels of the relationships and their description if available.</p>", "links"=>[], "tags"=>["imported"], "article_id"=>217324, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t007", "stats"=>{"downloads"=>1, "page_views"=>64, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationships_imported_from_EFO_/217324", "title"=>"Relationships imported from EFO.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:02:04"}
• {"files"=>["https://ndownloader.figshare.com/files/547054"], "description"=>"<p>As an Example, we show how the liver cancer cell line Hep3B is represented by using CCONT. For each data element derived from a cell bank's database we evaluated if the data could be represented using CCONT's classes. In this specific example the data for the Hep3B cell line were extracted from the ATCC database.</p>", "links"=>[], "tags"=>["hep3b"], "article_id"=>217546, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t009", "stats"=>{"downloads"=>7, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_cell_line_Hep3B_using_CCONT_/217546", "title"=>"Representation of cell line Hep3B using CCONT.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:05:46"}
• {"files"=>["https://ndownloader.figshare.com/files/547081"], "description"=>"<p>To establish a common platform in the research network, these cell lines were chosen and procured centrally. These cell lines also serve as test items for CCONT.</p>", "links"=>[], "tags"=>["lines", "cancer"], "article_id"=>217579, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t008", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cell_lines_used_in_the_liver_cancer_research_network_/217579", "title"=>"Cell lines used in the liver cancer research network.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:06:19"}
• {"files"=>["https://ndownloader.figshare.com/files/547020"], "description"=>"<p>The databases of five widely used cell banks were included into the comparison of data fields. The table shows the name of the Internet addresses were they can be reached. The Internet addresses were last accessed on March 1, 2012.</p>", "links"=>[], "tags"=>["banks"], "article_id"=>217516, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_cell_banks_compared_/217516", "title"=>"List of cell banks compared.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:05:16"}
• {"files"=>["https://ndownloader.figshare.com/files/546763"], "description"=>"<p>The class ‘supplement’ is defined in CCONT to identify substances that are necessary to support the growth of cell lines in culture. In other words, these substances are assigned specific roles in the process of cell culturing. As a consequence, we decided to place the ‘supplement’ class below EFO's ‘growth condition’ class in the ‘Role’ subtree.</p>", "links"=>[], "tags"=>["subtree"], "article_id"=>217263, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_8216_supplement_8217_subtree_of_CCONT_/217263", "title"=>"The ‘supplement’ subtree of CCONT.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 02:01:03"}
• {"files"=>["https://ndownloader.figshare.com/files/293025", "https://ndownloader.figshare.com/files/293106"], "description"=>"<div><p>Cell lines are frequently used as highly standardized and reproducible <em>in vitro</em> models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called <em>cell culture ontology (CCONT)</em> integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.</p> </div>", "links"=>[], "tags"=>["ontology", "based", "lines"], "article_id"=>117683, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048584.s001", "https://dx.doi.org/10.1371/journal.pone.0048584.s002"], "stats"=>{"downloads"=>28, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/On_the_Ontology_Based_Representation_of_Cell_Lines__/117683", "title"=>"On the Ontology Based Representation of Cell Lines", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-07 02:08:03"}
• {"files"=>["https://ndownloader.figshare.com/files/546927"], "description"=>"<p>The table lists data elements derived from cell banks. The last three columns show, which of the cell line related ontologies have classes that cover the data elements: full coverage, partial coverage, not covered.</p>", "links"=>[], "tags"=>["fields"], "article_id"=>217428, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_data_fields_in_cell_bank_databases_/217428", "title"=>"Sample data fields in cell bank databases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:03:48"}
• {"files"=>["https://ndownloader.figshare.com/files/546667"], "description"=>"<p>The ‘Quality’ class was originally defined as a child class to ‘material property’ in BFO. Since it is part of EFO it is also imported into CCONT. In CCONT we define several child-classes to ‘Quality’: ‘growth mode’, ‘safety classification’ and ‘cytogenetics’.</p>", "links"=>[], "tags"=>["subtree"], "article_id"=>217161, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_8216_Quality_8217_subtree_of_CCONT_/217161", "title"=>"The ‘Quality’ subtree of CCONT.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:59:21"}
• {"files"=>["https://ndownloader.figshare.com/files/546599"], "description"=>"<p>Technically, for the definition of CCONT we started with a fresh OWL file. Following the considerations described in this article, we reused the two ontologies EFO and IEV's event ontology. This is reflected by corresponding XML namespace definitions and OWL import statements.</p>", "links"=>[], "tags"=>["owl"], "article_id"=>217095, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_head_of_CCONT_s_OWL_file_/217095", "title"=>"The head of CCONT's OWL file.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:58:15"}
• {"files"=>["https://ndownloader.figshare.com/files/546525"], "description"=>"<p>This diagram shows some of CCONT's high-level classes to illustrate the structure of CCONT. The diagram is noted using the ontology profile of the Unified Modeling Language (UML, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Object1\" target=\"_blank\">[40]</a>). UML diagrams provide a standardized way to represent ontologies graphically <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Kogut1\" target=\"_blank\">[41]</a>. Classes in green color are imported from the EFO ontology. The class ‘Medium condition’, colored in blue, represents the corresponding subtree imported from INOH's event ontology. Classes newly defined in CCONT are shown in beige. Note that the EFO ontology incorporates other ontologies like BFO or OBO. This is represented by a corresponding UML package name. To ensure the legibility of the diagram we only show subClassOf relations.</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "cell biology", "computer science", "developmental biology", "Non-clinical medicine"], "article_id"=>217012, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structure_of_CCONT_/217012", "title"=>"The structure of CCONT.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:56:52"}
• {"files"=>["https://ndownloader.figshare.com/files/546858"], "description"=>"<p>Chemical compounds play different roles for the growth of cell lines. In column two we show how many compounds are necessary for describing a specific role. Column three shows the respective number of roles already present in EFO.</p>", "links"=>[], "tags"=>["compounds"], "article_id"=>217354, "categories"=>["Biotechnology", "Developmental Biology", "Information And Computing Sciences", "Biological Sciences", "Medicine", "Cell Biology"], "users"=>["Matthias Ganzinger", "Shan He", "Kai Breuhahn", "Petra Knaup"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048584.t006", "stats"=>{"downloads"=>0, "page_views"=>90, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_chemical_compounds_for_each_role_in_CCONT_/217354", "title"=>"Number of chemical compounds for each role in CCONT.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:02:34"}

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Relative Metric

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F1000Prime