CN115712643A - Metabolic path query method, device, equipment and storage medium - Google Patents
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Abstract
The invention provides a metabolic pathway query method, a device, equipment and a storage medium. One embodiment of the method comprises: obtaining omics data to be queried and the name of an entity to be queried; mapping the omics data to be queried to entity nodes in a preset metabolic network, wherein the preset metabolic network comprises at least two entity nodes, and each entity node corresponds to an entity node type; generating a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried; and inquiring a metabolic path taking an entity node corresponding to the name of the entity to be inquired as a starting point in the mapped metabolic network. The method realizes the query of the metabolic path in the graph database and has good accuracy and efficiency.
Description
Technical Field
The invention relates to the field of data query, in particular to a metabolic pathway query method, a metabolic pathway query device, metabolic pathway query equipment and a storage medium.
Background
With the development of computer technology, establishing an effective information system to fully and effectively manage and utilize various information resources is a precondition for scientific research and decision management, and thus, database technology serving as the core and the basis of the information system is more and more widely applied.
In the field of biomedicine, an important task in system biology is the analysis, annotation, and ligation of biochemical reactions. With the increasing number of known biochemical reactions, the traditional means of studying metabolic reaction pathways are increasingly inadequate. The construction of a genome-scale metabolic model such as Human-GEM promotes the simulation of metabolic reaction of computational biology, but similar models still need a large amount of manual arrangement and maintenance, and different models are difficult to integrate and analyze due to non-uniform format specifications. In addition, the development of technical means such as genomics, metabonomics, transcriptomics, etc. and the increase in data size have made early detection of various diseases possible in recent years. Therefore, it is urgent to develop a method for mapping and integrating analysis of multiple sets of chemical data on metabolic reaction pathways, particularly, for querying metabolic pathways.
Disclosure of Invention
The invention provides a metabolic pathway query method which can be used for solving the problems of low query efficiency and long operation time in the related technology.
In a first aspect, an embodiment of the present invention provides a metabolic pathway query method, where the method includes: obtaining omics data to be queried and the name of an entity to be queried; mapping the omics data to be queried to entity nodes in a preset metabolic network, wherein the preset metabolic network comprises at least two entity nodes, and each entity node corresponds to an entity node type; generating a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried; and inquiring a metabolic path taking an entity node corresponding to the name of the entity to be inquired as a starting point in the mapped metabolic network.
In some optional embodiments, after the generating the post-map metabolic network, the method further comprises: calculating the reaction activity level of the entity node with the node type as the reaction node in the mapped metabolic network; and after the mapped metabolic network queries a metabolic path with an entity node corresponding to the name of the entity to be queried as a starting point, the method further comprises: for each metabolic pathway queried, the following pathway score calculation operations are performed: determining a first index value of the metabolic path based on the similarity between the starting metabolite node and the ending metabolite node of the metabolic path; determining a second index value of the metabolic path based on the reactivity level corresponding to the reaction node in the metabolic path; determining a third index value of the metabolic path based on the path length of the metabolic path; and carrying out weighted summation on the first index value, the second index value and the third index value of the metabolic path according to the first preset weight, the second preset weight and the third preset weight to obtain the path score of the metabolic path.
In some optional embodiments, the method further comprises: determining metabolic pathways with the pathway scores meeting preset scoring conditions in all the metabolic pathways obtained through query as query result metabolic pathways; and outputting the metabolic paths of the query results.
In some optional embodiments, the metabolic network has nodes and connection relationships between nodes, where a plurality of the nodes are directionally connected based on the preset entity relationship, where the node types include: reaction nodes, pathway nodes, metabolite nodes, gene product group nodes, gene product complex nodes, cellular compartment nodes, citation nodes, species nodes, additional information nodes.
In some optional embodiments, the calculating the activity level of the entity node whose node type is a response node in the metabolic network after mapping includes: for each reaction node in the mapped metabolic network described above, the following activity level calculation operations are performed: taking the reaction node as a root node, and performing depth-first search or breadth-first search in the mapped metabolic network to obtain a search path; determining gene product nodes included in each obtained search path; for each determined gene product node, determining a source entity node corresponding to the gene product node, wherein a connecting line pointing to the gene product node from the source entity node corresponding to the gene product node exists in the mapped metabolic network, and the source entity node is a gene product group node or a gene product complex node; and calculating the activity level corresponding to the reaction node according to a preset calculation rule based on the obtained node data of each source entity node.
In some alternative embodiments, the name of the entity to be queried is a name of a metabolite entity to be queried, and the predetermined entity relationship is a consumption metabolic reaction; and the querying of the metabolic path with the entity node corresponding to the name of the entity to be queried as the starting point in the mapped metabolic network comprises: and querying a metabolic path taking a metabolite entity node corresponding to the name of the entity to be queried as a starting point and an end point in the mapped metabolic network, and responding to the condition that at least one query termination condition is met in the metabolic path query process, and ending the metabolic path query.
In some optional embodiments, the at least one termination query condition includes: the metabolic pathway reaches a preset length; the current end point entity node of the metabolic path is a metabolite node, and a connecting line which takes the current end point entity node as a starting point and takes the reaction node as an end point does not exist in the mapped metabolic network; the reaction node or metabolite node passed by the metabolic path belongs to a preset blacklist entity node set.
In a second aspect, an embodiment of the present invention provides a metabolic pathway query device, including: the acquisition unit is configured to acquire omics data to be queried and the name of an entity to be queried; the mapping unit is configured to map the omics data to be queried to entity nodes in a preset metabolic network, and the preset metabolic network comprises at least two entity nodes; the generating unit is configured to generate a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried; and the query unit is configured to query a metabolic path with an entity node corresponding to the name of the entity to be queried as a starting point in the mapped metabolic network.
In a third aspect, an embodiment of the present invention provides an electronic device, including: one or more processors; a storage device, on which one or more programs are stored, which, when executed by the one or more processors, cause the one or more processors to implement the method as described in any implementation manner of the first aspect.
In a fourth aspect, an embodiment of the present invention provides a computer-readable storage medium, on which a computer program is stored, where the computer program, when executed by one or more processors, implements the method as described in any implementation manner of the first aspect.
In order to improve the effect of the existing metabolic path query method, the device, the electronic device and the storage medium provided by the embodiment of the invention construct a metabolic network by mapping multiple sets of mathematical data transmitted by a user onto corresponding nodes of a graph database, search for possible paths consuming the metabolites in a reaction network when the metabolites (to-be-queried entity names) are given, firstly, search is performed according to entity relations in the graph database from the given metabolite nodes, and all possible reaction paths consuming the metabolites are returned. For all possible response paths returned, then scoring is performed according to the reactivity level in each path, the structure similarity degree of the final metabolite and the initial metabolite and the path length under the weight given by the user, and the path with the highest final score is returned as the metabolic path result. The method realizes the query of the metabolic path in the graph database and has good accuracy and efficiency.
Drawings
Other features, objects and advantages of the invention will become more apparent upon reading of the following detailed description of non-limiting embodiments thereof, made with reference to the accompanying drawings. The drawings are only for purposes of illustrating the particular embodiments and are not to be construed as limiting the invention. In the drawings:
FIG. 1 is an exemplary system architecture diagram in which one embodiment of the present invention may be applied.
FIG. 2 is a flow chart of one embodiment of a metabolic pathway query method according to the present invention.
FIG. 3 is a schematic structural diagram of an embodiment of a metabolic pathway query device according to the present invention.
FIG. 4 is a schematic block diagram of a computer system suitable for use with the electronic device to implement an embodiment of the invention.
Detailed Description
The present invention will be described in further detail with reference to the drawings and examples. It is to be understood that the specific embodiments described herein are merely illustrative of the relevant invention and not restrictive of the invention. It should be noted that, for convenience of description, only the portions related to the related invention are shown in the drawings.
It should be noted that the features of the examples and embodiments of the present invention may be combined with each other without conflict. The present invention will be described in detail below with reference to the embodiments with reference to the attached drawings.
FIG. 1 is a schematic diagram of an implementation environment of a metabolic pathway query method, apparatus, electronic device and storage medium to which the present invention may be applied.
As shown in fig. 1, the implementation environment includes an electronic device 100, and the metabolic pathway query method in the embodiment of the present invention may be executed by terminal devices 101, 102, 103, and 104. Illustratively, the electronic device 100 may comprise at least one of a terminal device or a server.
The terminal apparatuses 101, 102, 103, and 104 may be hardware or software. When the terminal devices 101, 102, 103, 104 are hardware, they may be various electronic devices having a display screen and supporting information input (e.g., text input and/or voice input, etc.), including but not limited to, smart phones, tablet computers, laptop portable computers, desktop computers, and the like. When the terminal apparatuses 101, 102, 103, and 104 are software, they can be installed in the above-listed terminal apparatuses. It may be implemented as a plurality of software or software modules (for example, to provide a metabolic pathway query service), or as a single software or software module. And is not particularly limited herein.
It should be understood that the number of terminal devices in fig. 1 is merely illustrative. There may be any number of terminal devices, as desired for implementation.
With continued reference to FIG. 2, a flowchart 200 of one embodiment of a metabolic pathway query method according to the present invention is shown, the metabolic pathway query method comprising the steps of:
In this embodiment, the executing entity of the metabolic pathway query method may first obtain omics data to be queried and a name of an entity to be queried. The embodiments of the present invention do not limit the omics data to be queried, and exemplary omics data to be queried include, but are not limited to, genomic data, transcriptomic data, and proteomic data. The embodiment of the present invention also does not limit the name of the entity to be queried, for example, the name of the entity to be queried is a metabolite name and the like, and the metabolite name includes a metabolic substrate name and a metabolic product name.
The predetermined metabolic network includes at least two entity nodes, wherein each entity node corresponds to an entity node type.
In some optional embodiments, the metabolic network has nodes and connection relationships between nodes, wherein a plurality of the nodes are directionally connected based on the predetermined entity relationship, and the node types include: reaction nodes, pathway nodes, metabolite nodes, gene product group nodes, gene product complex nodes, cellular compartment nodes, citation nodes, species nodes, additional information nodes.
As an example, table 1 shows parameter names and field meanings of each field in the step of mapping the omics data to be queried to entity nodes in the preset metabolic network.
Table 1 omics data mapping parameter table
And step 203, generating a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried.
In some alternative embodiments, the executing agent of the metabolic pathway query method may further execute the following step 203' after executing step 203:
and step 203', calculating the reaction activity level of the entity node with the node type as the reaction node in the metabolic network after mapping.
In this embodiment, the execution main body of the metabolic pathway query method first performs depth-first search or breadth-first search in the mapped metabolic network by using the reaction node as a root node to obtain a search pathway; determining gene product nodes included in each obtained search path; for each determined gene product node, determining a source entity node corresponding to the gene product node, wherein a connecting line pointing to the gene product node from the source entity node corresponding to the gene product node exists in the mapped metabolic network, and the source entity node is a gene product group node or a gene product complex node; and calculating the activity level corresponding to the reaction node according to a preset calculation rule based on the obtained node data of each source entity node.
And step 204, inquiring a metabolic path taking an entity node corresponding to the name of the entity to be inquired as a starting point in the mapped metabolic network.
In some alternative embodiments, the executing entity of the metabolic pathway query method may further execute the following steps 205 to 209 after executing step 204:
in step 205, for each of the queried metabolic pathways, a pathway score calculation operation is performed.
Here, the path score calculating operation may specifically include: and determining a first index value of the metabolic path based on the similarity between the starting metabolite node and the ending metabolite node of the metabolic path.
At step 206, a second index value of the metabolic pathway is determined based on the reactivity level corresponding to the reaction node in the metabolic pathway.
And step 208, carrying out weighted summation on the first index value, the second index value and the third index value of the metabolic pathway according to the first preset weight, the second preset weight and the third preset weight to obtain a pathway score of the metabolic pathway.
And step 209, determining the metabolic pathways with the pathway scores meeting the preset scoring conditions in the various metabolic pathways obtained by the query as the metabolic pathways of the query result.
In some optional embodiments, the main body of the metabolic path query method queries a metabolic path with a metabolite entity node corresponding to the name of the entity to be queried as a start point and an end point in the post-mapping metabolic network, and ends the metabolic path query in response to at least one query termination condition being met in the metabolic path query process.
In this embodiment, the termination query condition is not limited, and for example, the termination query condition includes but is not limited to: the metabolic pathway reaches a preset length; the current end point entity node of the metabolic pathway is a metabolite node, and a connecting line which takes the current end point entity node as a starting point and takes the reaction node as an end point does not exist in the mapped metabolic network; the reaction node or metabolite node passed by the metabolic path belongs to a preset blacklist entity node set.
As an example, table 2 shows parameter names and field meanings of each field in the step of querying the metabolic path with the metabolite entity node corresponding to the name of the entity to be queried as the start point and the end point in the mapped metabolic network.
TABLE 2 Metabolic Path query parameters Table
With further reference to fig. 3, as an implementation of the methods shown in the above figures, the present invention provides an embodiment of a metabolic pathway query apparatus, where the embodiment of the apparatus corresponds to the embodiment of the method shown in fig. 2, and the apparatus can be specifically applied to various electronic devices.
As shown in fig. 3, the metabolic pathway query device 300 of the present embodiment includes: an acquisition unit 301, a mapping unit 302, a generation unit 303 and a query unit 304. The obtaining unit 301 is configured to obtain omics data to be queried and names of entities to be queried; a mapping unit 302, configured to map the omics data to be queried to entity nodes in a preset metabolic network, where the preset metabolic network includes at least two entity nodes; a generating unit 303, configured to generate a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried; the query unit 304 is configured to query a metabolic path with an entity node corresponding to the name of the entity to be queried as a starting point in the mapped metabolic network.
In this embodiment, the specific processes of the obtaining unit 301, the mapping unit 302, the generating unit 303 and the querying unit 304 of the metabolic pathway query device 300 and the technical effects thereof can refer to the related descriptions of step 201, step 202, step 203 and step 204 in the corresponding embodiment of fig. 2, which are not repeated herein.
As shown in fig. 4, a schematic diagram of a computer system 400 suitable for use in implementing the electronic device of the present invention is shown. The computer system 400 illustrated in FIG. 4 is only an example and should not impose any limitations on the scope of use or functionality of embodiments of the invention.
As shown in fig. 4, computer system 400 may include a processing device (e.g., central processing unit, graphics processor, etc.) 401 that may perform various suitable actions and processes in accordance with a program stored in a Read Only Memory (ROM) 402 or a program loaded from a storage device 408 into a Random Access Memory (RAM) 403. In the RAM 403, various programs and data necessary for the operation of the computer system 400 are also stored. The processing device 401, the ROM402, and the RAM 403 are connected to each other via a bus 404. An input/output (I/O) interface 405 is also connected to bus 404.
Generally, the following devices may be connected to the I/O interface 405: input devices 406 including, for example, a touch screen, touch pad, keyboard, mouse, camera, microphone, etc.; an output device 407 including, for example, a Liquid Crystal Display (LCD), a speaker, a vibrator, and the like; storage 408 including, for example, tape, hard disk, etc.; and a communication device 409. The communication device 409 may allow the computer system 400 to communicate with other devices, either wirelessly or by wire, to exchange data. While fig. 4 illustrates a computer system 400 having various means of electronic equipment, it is to be understood that not all illustrated means are required to be implemented or provided. More or fewer devices may be alternatively implemented or provided.
In particular, according to an embodiment of the present invention, the processes described above with reference to the flowcharts may be implemented as computer software programs. For example, embodiments of the invention include a computer program product comprising a computer program embodied on a computer-readable medium, the computer program comprising program code for performing the method illustrated in the flow chart. In such an embodiment, the computer program may be downloaded and installed from a network via the communication device 409, or from the storage device 408, or from the ROM 402. The computer program, when executed by the processing apparatus 401, performs the functions defined above in the methods of embodiments of the present invention.
It should be noted that the computer readable medium of the present invention can be a computer readable signal medium or a computer readable storage medium or any combination of the two. A computer readable storage medium may be, for example, but not limited to, an electronic, magnetic, optical, electromagnetic, infrared, or semiconductor system, apparatus, or device, or any combination of the foregoing. More specific examples of the computer readable storage medium may include, but are not limited to: an electrical connection having one or more wires, a portable computer diskette, a hard disk, a Random Access Memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or flash memory), an optical fiber, a portable compact disc read-only memory (CD-ROM), an optical storage device, a magnetic storage device, or any suitable combination of the foregoing. In the present invention, a computer readable storage medium may be any tangible medium that can contain, or store a program for use by or in connection with an instruction execution system, apparatus, or device. In contrast, in the present invention, a computer readable signal medium may include a propagated data signal with computer readable program code embodied therein, for example, in baseband or as part of a carrier wave. Such a propagated data signal may take many forms, including, but not limited to, electro-magnetic, optical, or any suitable combination thereof. A computer readable signal medium may also be any computer readable medium that is not a computer readable storage medium and that can communicate, propagate, or transport a program for use by or in connection with an instruction execution system, apparatus, or device. Program code embodied on a computer readable medium may be transmitted using any appropriate medium, including but not limited to: electrical wires, optical cables, RF (radio frequency), etc., or any suitable combination of the foregoing.
The computer readable medium may be embodied in the electronic device; or may exist separately without being assembled into the electronic device.
The computer readable medium carries one or more programs which, when executed by the electronic device, cause the electronic device to implement the metabolic pathway query method as shown in the embodiment shown in fig. 2 and its alternative embodiments.
Computer program code for carrying out operations for aspects of the present invention may be written in any combination of one or more programming languages, including an object oriented programming language such as Java, smalltalk, C + + or the like and conventional procedural programming languages, such as the "C" programming language or similar programming languages. The program code may execute entirely on the user's computer, partly on the user's computer, as a stand-alone software package, partly on the user's computer and partly on a remote computer or entirely on the remote computer or server. In the case of a remote computer, the remote computer may be connected to the user's computer through any type of network, including a Local Area Network (LAN) or a Wide Area Network (WAN), or the connection may be made to an external computer (for example, through the Internet using an Internet service provider).
The flowchart and block diagrams in the figures illustrate the architecture, functionality, and operation of possible implementations of systems, methods and computer program products according to various embodiments of the present invention. In this regard, each block in the flowchart or block diagrams may represent a module, segment, or portion of code, which comprises one or more executable instructions for implementing the specified logical function(s). It should also be noted that, in some alternative implementations, the functions noted in the block may occur out of the order noted in the figures. For example, two blocks shown in succession may, in fact, be executed substantially concurrently, or the blocks may sometimes be executed in the reverse order, depending upon the functionality involved. It will also be noted that each block of the block diagrams and/or flowchart illustration, and combinations of blocks in the block diagrams and/or flowchart illustration, can be implemented by special purpose hardware-based systems which perform the specified functions or acts, or combinations of special purpose hardware and computer instructions.
The units described in the embodiments of the present invention may be implemented by software or hardware. Where the name of an element does not in some cases constitute a limitation on the element itself.
The foregoing description is only exemplary of the preferred embodiments of the invention and is illustrative of the principles of the technology employed. It will be appreciated by those skilled in the art that the scope of the disclosure herein is not limited to the particular combination of features described above, but also encompasses other embodiments in which any combination of the features described above or their equivalents is encompassed without departing from the spirit of the disclosure. For example, the above features and the technical features (but not limited to) having similar functions disclosed in the present invention are mutually replaced to form the technical solution.
Claims (10)
1. A metabolic pathway query method, the method comprising:
acquiring omics data to be queried and a name of an entity to be queried;
mapping the omics data to be queried to entity nodes in a preset metabolic network, wherein the preset metabolic network comprises at least two entity nodes, and each entity node corresponds to an entity node type;
generating a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried;
and inquiring a metabolic path taking an entity node corresponding to the name of the entity to be inquired as a starting point in the mapped metabolic network.
2. The method of claim 1, after the generating a mapped metabolic network, the method further comprising:
calculating the reaction activity level of the entity node with the node type as the reaction node in the mapped metabolic network; and
after querying a metabolic path with an entity node corresponding to the name of the entity to be queried as a starting point in the mapped metabolic network, the method further comprises:
for each metabolic pathway queried, the following pathway score calculation operations are performed:
determining a first index value of the metabolic path based on the similarity between the starting metabolite node and the ending metabolite node of the metabolic path;
determining a second index value of the metabolic path based on the reactivity level corresponding to the reaction node in the metabolic path;
determining a third index value of the metabolic path based on the path length of the metabolic path;
and carrying out weighted summation on the first index value, the second index value and the third index value of the metabolic path according to the first preset weight, the second preset weight and the third preset weight to obtain the path score of the metabolic path.
3. The method of claim 2, wherein the method further comprises:
determining metabolic paths with path scores meeting preset scoring conditions in all the metabolic paths obtained through query as query result metabolic paths;
and outputting each inquiry result metabolic path.
4. The method of claim 1, wherein the metabolic network has nodes and connection relationships between nodes, wherein a plurality of the nodes are directionally connected based on the predetermined entity relationship, wherein the node types include: reaction nodes, pathway nodes, metabolite nodes, gene product group nodes, gene product complex nodes, cellular compartment nodes, citation nodes, species nodes, additional information nodes.
5. The method of claim 2, the calculating a level of reactivity of an entity node in the post-mapping metabolic network having a node type of a reaction node, comprising:
for each reaction node in the mapped metabolic network, performing the following activity level calculation operations: taking the reaction node as a root node, and performing depth-first search or breadth-first search in the mapped metabolic network to obtain a search path; determining gene product nodes included in each obtained search path; for each determined gene product node, determining a source entity node corresponding to the gene product node, wherein a connecting line pointing to the gene product node from the source entity node corresponding to the gene product node exists in the mapped metabolic network, and the source entity node is a gene product group node or a gene product complex node; and calculating the activity level corresponding to the reaction node according to a preset calculation rule based on the obtained node data of each source entity node.
6. The method according to claim 1, wherein the name of the entity to be queried is the name of a metabolite entity to be queried, and the preset entity relationship is a consumption metabolic reaction; and
the querying of the metabolic path with the entity node corresponding to the name of the entity to be queried as the starting point in the mapped metabolic network comprises:
and inquiring a metabolic path taking a metabolite entity node corresponding to the name of the entity to be inquired as a starting point and an end point in the mapped metabolic network, and ending the metabolic path inquiry in response to the metabolic path inquiry process meeting at least one termination inquiry condition.
7. The method of claim 6, wherein the at least one termination query condition comprises: the metabolic pathway reaches a preset length; the current end point entity node of the metabolic path is a metabolite node, and a connecting line which takes the current end point entity node as a starting point and takes the reaction node as an end point does not exist in the mapped metabolic network; and the reaction nodes or metabolite nodes passed by the metabolic paths belong to a preset blacklist entity node set.
8. A metabolic pathway query device comprising:
the system comprises an acquisition unit, a query unit and a query unit, wherein the acquisition unit is configured to acquire omics data to be queried and entity names to be queried;
a mapping unit configured to map the omics data to be queried to entity nodes in a preset metabolic network, wherein the preset metabolic network comprises at least two entity nodes;
the generating unit is configured to generate a mapped metabolic network based on the preset metabolic network and each entity node mapped with the omics data to be queried;
and the query unit is configured to query a metabolic path with an entity node corresponding to the name of the entity to be queried as a starting point in the mapped metabolic network.
9. An electronic device, comprising:
one or more processors;
a storage device having one or more programs stored thereon,
the one or more programs, when executed by the one or more processors, cause the one or more processors to implement the method of any of claims 1-7.
10. A computer-readable storage medium, having stored thereon a computer program, wherein the computer program, when executed by one or more processors, implements the method of any one of claims 1-7.
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