KR101488338B1 - method for combining biopathways, apparatus for combining biopathways and storage medium for storing a program combining biopathways - Google Patents

Abstract

The purpose of the present invention is to effectively combine biopathways that are expressed in different languages as biopathways are constructed separately and independently using various biopathway description languages such as KGML, SBML, BIOPAX, etc. by various biopathway-related institutions. For the purpose, the present invention comprises the steps of: receiving a biopathway (S90); converting the biopathway into a first language (S91); separating the biopathway (S92); standardizing the node or relation of the biopathway in a standard term, storing the biopathway by using the node or the relation and extracting attribute information relating to the node or the relation (S93); searching the biopathway (S94); and combining a plurality of biopathways (S95).

Description

FIELD OF THE INVENTION [0001] The present invention relates to a device for biopathway integration, a method thereof, and a storage medium storing a program for integrating the biopathways,

The present invention relates to an apparatus for integrating a bio-pathway, a method thereof, and a storage medium storing a program for integrating bio-paths.

Bioinformatics is a combination of biotechnology (bio) and information engineering (informatics). It uses computers and software to collect, analyze, manage and utilize gene sequence data. It is also called bioinformatics. Recently, with the completion of the human genome project, the amount of data to be managed has increased as the amount of genetic information has increased, and the importance of bioinformatics has increased. With the development of bioinformatics, bio-related information is growing exponentially, and research subjects include DNA pathways for how functions are performed by DNA, RNA, proteins, and their interaction and control mechanisms. . The bio-pathway encompasses vast amounts of information and represents an organic relationship between constituents. In the field of biology, high quality biopathway databases can be used to understand the mechanisms of life activity of various organisms, to identify the causes of disease, progress, natural extinction and physical causes of healing. In addition to efficient research and development in the field of biotechnology, there are substantial advantages in terms of knowledge services. However, various biopathway-related institutes independently construct various biopathway language (KGML, SBML, BIOPAX, etc.) There are many problems and limitations in terms of building, linking and utilizing bio-pathway database. Also, since most of the bio-pathway databases are built by hand, they require enormous construction costs and can not be expanded or changed quickly in accordance with technological development.

SUMMARY OF THE INVENTION The present invention has been made to solve the above-mentioned problems, and it is an object of the present invention to provide a device for integrating a biopathway to effectively integrate a biopathway expressed in a heterogeneous language, a method thereof, and a storage medium storing a program for integrating biopathways The purpose is to provide.

In order to achieve the above object, according to a first aspect of the present invention, there is provided a bio-pathway integrating apparatus comprising: an input module receiving at least one bio-pathway input; A language unification module for converting the at least one biopathway into a first language; A separation module for separating the biopathways converted into the first language, and the separation module separating the biopathways converted into the first language into nodes or relations; A standardization module for standardizing the node or relation in standard terms, storing a bio-pathway converted into the first language in the form of the node or relationship, and extracting attribute information related to the node or relationship; And an integration module for integrating a plurality of the stored bio-pathways.

 According to a second aspect of the present invention, there is provided a method of generating a bio-pathway, comprising: receiving at least one bio-pathway input; Converting the at least one bio-pathway into a first language; Separating the biopathways converted into the first language, and separating comprises separating the biopathways converted into the first language into nodes or relationships; Standardizing the node or relationship in standard terms, storing the biopathic way translated into the first language in the form of the node or relationship, and extracting attribute information related to the node or relationship; And integrating a plurality of the stored bio-pathways.

 According to a third aspect of the present invention, there is provided a bio-pathway management method comprising: receiving at least one bio-pathway input, converting the at least one bio-pathway into a first language, Extracting attribute information related to the node or relationship, storing a plurality of the stored nodes or relationships in a standard language, storing a biopathway converted into the first language in the form of the node or relationship, And a storage medium storing a program for integrating the biopathways.

As described above, according to the present invention, it is possible to efficiently construct a bio-pathway database at a low cost by providing a device for integrating a bio-pathway, a method thereof, and a storage medium storing a program for integrating bio-paths.

A device for biopathway integration, a method thereof, and a storage medium for storing a program for integrating biopathways are provided, whereby a new pathogenic mechanism can be extracted through deep knowledge extraction through an integrated pathway.

Also, by providing a storage medium storing a device for integrating a bio pathway, a method thereof, and a program for integrating a biopathway, rapid expansion and modification of the database can be performed in accordance with technological development.

BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 is a schematic flow diagram illustrating an apparatus for integrating a bio-pathway, a method thereof, and a storage medium storing a program for integrating bio-paths according to an embodiment of the present invention;
FIG. 2 is a block diagram illustrating a device for integrating a bio-pathway according to an embodiment of the present invention. FIG.
3 is a diagram illustrating an overall process of integrating a bio-pathway according to an embodiment of the present invention;
FIG. 4 is a diagram illustrating input bio-pathway information and all stored bio-pathway information according to an embodiment of the present invention; FIG.
FIG. 5 is a view showing another inputted bio-pathway information and all stored bio-pathway information according to an embodiment of the present invention; FIG.
FIG. 6 is a view showing integrated bio-pathway information and stored bio-pathway information according to an embodiment of the present invention; FIG.
FIG. 7 is a diagram illustrating a bio-pathway of Alzheimer's disease according to an embodiment of the present invention;
FIG. 8 is a diagram illustrating a bio-pathway expressed in the KGML language according to an embodiment of the present invention;
9 is a flowchart illustrating a bio-pathway integration method according to an embodiment of the present invention.

One embodiment of the present invention will be described in detail with reference to the accompanying drawings. In the following description of the present invention, a detailed description of known functions and configurations incorporated herein will be omitted when it may make the subject matter of the present invention rather unclear.

FIG. 1 is a schematic flowchart for explaining an apparatus for integrating a bio-pathway, a method thereof, and a storage medium for storing a program for integrating bio-paths according to an embodiment of the present invention.

Referring to FIG. 1, the bio-pathway integration according to the present invention includes a bio-pathway input 10, a language unification unit 11 for unifying in one language, a bio-pathway unified in one language as a node or relationship A storage unit 12 for separating and storing standardized standard terms and storing them, a search unit 13 for searching for a desired biopathway for integration, and an integration generating unit 14 for integrating a plurality of biopathways.

2 is a block diagram illustrating an apparatus for integrating a bio-pathway according to an embodiment of the present invention.

2, an apparatus for integrating a bio-pathway according to the present invention includes an input module 20, a language unification module 21, a separation module 22, a standardization module 23, a search module 24, And an integration module 25. The input module 20 receives the bio-pathway input desired to be integrated.

The language unification module 21 unifies bio pathways expressed in a heterogeneous language in various institutions in one language. The heterogeneous languages include KGML, SBML, BIOPAX, and PSI-MI. SBML is used to unify bio-pathways expressed in heterogeneous languages into one language, but it can be changed according to the user's intention or new language can be created. The unified biopathway in one language can be stored in the biopathway DB 26 for use in making future integrated biopathways.

The separation module 22 separates the biopathway into nodes or relationships. Examples of nodes are proteins, enzymes, genes, etc. The relationship is a mechanism between nodes and nodes. Examples include activation, expression, and metastasis. Specifically, it is desirable to convert the bio-pathway into a triple-type node-relation-node type, but the separation type can be changed according to the user's intention and is not limited to the triple type. For reference, the separation module uses the information DB 27 to obtain necessary information for separating a node or a relation from the bio-pathway as a whole, such as checking whether a node or a relation is separated from the bio-pathway. In addition, the separated biopathway can be stored in the biopathway DB 26 in a separate form for use in making an integrated biopathway.

The standardization module 23 standardizes nodes or relationships into standard terms since the nodes or relationships separated from the unified biopathway in one language can be expressed in various terms even if they have substantially the same function. For example, in the case of ALDH1, which is a kind of protein, aldehyde dehydrogenase 1, Aldehyde dehydrogenase 1 family, member A1, ALHDII, ALDH-E1, Acetaldehyde dehydrogenase 1, Retinal dehydrogenase 1, RALDH 1, ALDC, and so on. In other words, the term represented by the above expression represents the same protein, but many users use different terms. For reference, the standardization module uses the information DB (27) to obtain information necessary for standardizing a separate node or relationship, such as mapping information for a dialect having the same meaning as the standard term but having different expressions, ) Is used. An example of the information DB is HPRD (Human Protein Reference Database), but it is not limited to this because it can be changed according to the user's intention. In addition, a bio-pathway can be stored in the biopathway DB 26 in the form of standardized nodes or relationships for use in making future integrated biopathways.

In addition, the standardization module 23 extracts attribute information related to a node or relationship separated from the biopathway. The property information includes the frequency of each node of the bio-pathway, the number of links per node, and the frequency of each relationship, and includes the frequency of all the nodes of the stored bio-pathway, the number of links of all nodes, and the frequency of each relationship. However, the kind of attribution information can be variously changed according to the intention of the user, and therefore, the present invention is not limited to the above. For reference, the standard module uses the biopathway DB 26 or the information DB 27 to acquire information that is generally required in extracting the attribute information. In addition, the extracted attribute information can be stored in the biopathway DB 26 for use in making an integrated biopathway.

The search module 24 searches for a bio pathway to be integrated. A specific search method searches based on exact match or similarity using nodes, relationships, triples (node-relation-node), part of a biopathway, and whole biopathway. However, the search method can be changed according to the intention of the user. For reference, the information DB 27 can be utilized to diversify the search method. The integration module 25 integrates the bio-pathway searched through the search module or the bio-pathway 28 arbitrarily designated by the user. The integration module integrates biopathways based on a triple (node-relationship-node) basis, but is not limited thereto and can be changed according to the user's intention. Also, the attribute information related to the node or relationship of the integrated pathway and the integrated pathway of the bio-pathway can be stored in the biopathway DB 26 for use in making another integrated pathway.

FIG. 3 is a diagram illustrating an overall process of integrating a bio-pathway according to an embodiment of the present invention.

Referring to FIG. 3, reference numeral 30 denotes a bio-pathway input to the input module 20, and reference numeral 31 denotes another bio-pathway input to the input module. Reference numerals 32 and 33 denote a common triple among those in which the inputted biopathways are separated into a node-relation-node, aka triple shape through a separation process. Specifically, the bio-pathway integration process will be described. The bio-pathways 30 and 31 are integrated into a single language, and are integrated based on a common triple through a separation process and a standardization process using standard terms. 3, the common triples of the input biopathways 30 and 31 are 'B-D' 32 and 33, and the inputted biopathways are 'B-D' 34, which is a common triple. .

FIG. 4 is a view showing input bio-pathway information and all stored bio-pathway information according to an embodiment of the present invention.

Referring to FIG. 4, reference numeral 40 denotes an input bio-pathway, and reference numeral 41 denotes a bio-pathway 40 separated into triples based on a node or a relation through a separation module. Reference numeral 42 denotes a common triple as described above in Fig. Reference numeral 43 denotes the number of nodes and the number of links per node, which are attribute information extracted in association with nodes or relationships of the input bio-pathway, and reference numeral 44 denotes frequencies per relationship. The attribute information is stored in the bio-pathway DB and reflected in the attribute information related to the node or relation of the bio-pathway already stored in the bio-pathway DB. Therefore, reference numeral 45 denotes the frequency of all the nodes and the number of links of all the nodes, which are attribute information extracted in association with the nodes or relationships of the bio-pathway stored in the bio-pathway DB, and reference numeral 46 denotes frequencies of the entire relationships. The node A of the bio-pathway 40 is connected to the nodes B, C, and D so that the number of links is three, There is only one node A in the biopathway, so the frequency is one. Since there is only one triplet (relation) 'B-D' in the input bio-pathway, the frequency is 1.

FIG. 5 is a diagram showing another inputted bio-pathway information and stored bio-pathway information according to an embodiment of the present invention.

Referring to FIG. 5, reference numeral 50 denotes an input bio-pathway, and reference numeral 51 denotes a bio-pathway 50 separated into triples based on nodes or relationships through a separation module. Reference numeral 52 denotes a common triple as described above in Fig. Reference numeral 53 denotes the frequency of each node and the number of links per node, which are attribute information extracted in association with the node or relationship of the inputted bio-pathway, and reference numeral 54 denotes the frequency of each relation. The attribute information is stored in the bio-pathway DB and reflected in the attribute information related to the node or relation of the bio-pathway already stored in the bio-pathway DB. Therefore, reference numeral 55 denotes the frequency of each node and the number of links of all the nodes, which are attribute information extracted in association with the node or relationship of the bio-pathway stored in the bio-pathway DB, and 56 denotes the frequency of each relation. Specifically, the node B of the input bio-pathway 50 is connected to the nodes D, E, and F, and the number of links is three, There is only one node B in the biopathway, so the frequency is one. Since there is only one triplet (relation) 'B-D' in the input bio-pathway, the frequency is 1. 5, since another bio-pathway 50 is additionally input in FIG. 5, the stored entire bio-pathway property information of FIG. 5 indicates that the node < RTI ID = 0.0 > The frequency 55 of B, the frequency 55 of the node D and the frequency 56 of the triple BD are increased by one compared with the stored biopathway overall property information of FIG.

FIG. 6 is a view showing integrated bio-pathway information and all stored bio-pathway information according to an embodiment of the present invention.

Referring to FIG. 6, reference numeral 63 denotes the number of links per node and the number of links per node, which are attribute information extracted in association with nodes or relationships of the integrated bio-pathway, and reference numeral 65 denotes frequency numbers per relationship. The attribute information is stored in the bio-pathway DB and reflected in the attribute information related to the node or relation of the bio-pathway already stored in the bio-pathway DB. Therefore, reference numeral 67 denotes the frequency of each node and the number of links of all the nodes, which are attribute information extracted in association with the node or relationship of the bio-pathway stored in the bio-pathway DB, and reference numeral 69 denotes the frequency of each relation. Specifically, referring to the attribute information related to the node or the relationship of the integrated bio-pathway, the node B of the integrated bio-pathway is connected to the nodes A, D, and E, and the number of links is three. Since the node D (62) exists in the bio-pathway before being integrated as described above with reference to FIGS. 4 and 5, the number of frequencies is two in the integrated bio-pathway. In addition, since 'B-D' 64, which is a triple (relationship) in the integrated bio-pathway, exists in each of the bio-pathways before integration as described above with reference to FIGS. 4 and 5, The frequency is two. In addition, referring to the entire attribute information related to the node or relation of the stored bio-pathway, the frequency 66 of the node D in FIG. 6 is significantly lower than that of the other nodes. This means that it is concentrated only on a specific biopathway, and is more important than all biopathways. Therefore, in order to show the importance, the node D is enlarged (61) compared with other nodes. In the case of the triple 'B-D' (68), it can be confirmed that the frequency is significantly lower than other triples, that is, other relation information. This means that it is concentrated only on a specific biopathway, and is a key mechanism that is more important than all biopathways, that is, key information. Therefore, triple 'B-D' is shown in bold (60) to indicate its importance. The expression system can be changed according to the intention of the user.

7 is a view illustrating a bio-pathway of Alzheimer's disease according to an embodiment of the present invention.

Referring to FIG. 7, reference numeral 70 denotes a node represented by a quadrangle in the bio-pathway, and reference numeral 71 denotes a relationship represented by an arrow in the bio-pathway.

FIG. 8 is a diagram illustrating a bio-pathway expressed in the KGML language according to an embodiment of the present invention.

Referring to FIG. 8, according to the present invention, FIG. 8 is an enlarged view of a portion of FIG. 7 to express the bio-pathway in the KGML language described above. The reference numeral 80 represents the 'FADD-> CASP80' triple, which can be represented by text (81) in XML. Specifically, the content after <graphics name> refers to node names (CAPS8 and 82), and the same terms such as CAPS8 and CASP-8, but other types of terms may be separated by a comma (,). These node names are standardized using the information DB and can also be used to expand the information DB 27.

In addition, the content following the <relation> means relation information (PPRel, 83). For example, PPRel stands for Protein Protein Relation, which means protein-protein relationship, and PCRel stands for Protein Compound Relation, which means protein-complex relationship.

9 is a flowchart illustrating a bio-pathway integration method according to an embodiment of the present invention.

 Referring to FIG. 9, the method of integrating a bio-pathway according to the present invention includes a step of receiving a bio-pathway input (S90), a step of converting a bio-pathway into a first language (S91) S92), standardizing the node or relationship of the bio-pathway with standard terms, storing the bio-pathway in the form of a node or relationship, extracting attribute information related to the node or relationship (S93), searching the bio- (S94), and integrating a plurality of biopathways (S95).

The input module 20 can be converted into a step S90 of receiving a bio-pathway input, and a detailed description thereof has been given above with reference to FIG.

The language unification module 21 can be converted into a step S91 of converting the bio-pathway into a first language, and a detailed description thereof has been given above with reference to FIG.

The separation module 22 can be converted into a step S92 of separating the bio-pathway, and a detailed description thereof has been given above with reference to FIGS. 2, 3, 4, 5 and 6. FIG.

The standardization module 23 can be converted to standardize the node or relationship of the bio-pathway in standard terms, store the bio-pathway in the form of nodes or relationships, and extract the attribute information related to the node or relationship (S93) A detailed description thereof has been given above with reference to Figs. 2, 3, 4, 5 and 6.

The search module 24 can be converted into a step S94 of searching for a biopathway, and a detailed description thereof has been given above with reference to FIG.

The integration module 25 can be converted into a step S95 of integrating a plurality of biopathways, and detailed description thereof has been given above with reference to FIGS. 2, 3, 4, 5 and 6.

The embodiments disclosed in the specification of the present invention do not limit the present invention. The scope of the present invention should be construed according to the following claims, and all the techniques within the scope of equivalents should be construed as being included in the scope of the present invention.

20: input module
21: Language Unification Module
22: Separation module
23: Standardization module
24: Search module
25: Integration module
26: Biopathway DB
27: Information DB

Claims (20)

An input module for receiving at least one bio-pathway input;
A language unification module for converting the at least one biopathway into a first language;
A separation module for separating the bio-pathways converted into the first language,
Wherein the separation module comprises separating the biopathways converted into the first language into nodes or relationships;
A standardization module for standardizing the node or relation in standard terms, storing a bio-pathway converted into the first language in the form of the node or relationship, and extracting attribute information related to the node or relationship; And
And an integration module for integrating a plurality of the stored bio-pathways. The bio-pathway integrated device according to claim 1,
Further comprising a retrieval module for retrieving the stored biopathway by using the whole of the biopathway, a node, a relation, a part of the biopathway, and a whole of the biopathway. The method of claim 1, wherein the at least one bio-
Wherein the network is expressed in a network constructed in a heterogeneous language. The method of claim 1, wherein the language unification module comprises:
And storing the converted bio-pathway. [2] The method of claim 1,
Node-relationship-node. &Lt; / RTI &gt; 2. The method of claim 1,
Node-relationship-node in a triple form. The method according to claim 1,
The number of links of each of the nodes, the number of links of each node, the frequency of each relation, the frequency of all the nodes of the stored bio pathway, the number of links of all the nodes, the frequency of each relation, A biopathway integrated device comprising: The information processing apparatus according to claim 1,
And integrating a plurality of biopathways selected by user selection or by searching. The information processing apparatus according to claim 1,
And storing the integrated bio-pathway. The information processing apparatus according to claim 1,
And integrating the bio-pathway based on the relationship information. The bio-pathway integrated device according to claim 1,
A biopathway integration device further comprising a biopathway DB and an information database. Receiving at least one biopathway input;
Converting the at least one bio-pathway into a first language;
Separating the bio-pathways converted into the first language,
Wherein the separating comprises separating the biopathic path translated into the first language into nodes or relationships;
Standardizing the node or relationship in standard terms, storing the biopathic way translated into the first language in the form of the node or relationship, and extracting attribute information related to the node or relationship; And
And integrating a plurality of the stored biopathways. 13. The bio-pathway integration method according to claim 12,
Further comprising the step of searching for the stored biopathway using the entire node, the relationship, a part of the biopathway, and the entire biopathway. The method of claim 12, wherein the converting the at least one biopathway into a first language comprises:
Further comprising the step of storing the converted biopathway. 13. The method of claim 12, wherein separating the biopathways converted into the first language comprises:
And separating the bio-pathway converted into the first language into a node-relationship-node form. 13. The method of claim 12, wherein standardizing the node or relationship to standard terms and storing a biopathic way translated into the first language in the form of the node or relationship, and extracting attribute information associated with the node or relationship ,
Further comprising the step of storing the standardized bio-pathway in a triple form such as a node-relationship-node. 13. The method according to claim 12,
The number of links of each of the nodes, the number of links of each node, the frequency of each relation, the frequency of all the nodes of the stored bio pathway, the number of links of all the nodes, the frequency of each relation, A method for integrating a bio-pathway. 13. The method of claim 12, wherein integrating the plurality of stored bio-
Integrating a plurality of biopathways selected by user selection or by searching. 13. The method of claim 12, wherein integrating the plurality of stored bio-
A biopathway integration method comprising integrating a bio-pathway based on relationship information. The method comprising the steps of: receiving at least one bio-pathway input, converting the at least one bio-pathway into a first language, separating the bi-pathway translated into the first language into nodes or relationships, , Storing a biopathway converted into the first language in the form of the node or relationship, extracting attribute information related to the node or relationship, and integrating a plurality of the stored biopathways Storage medium.

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