The Lipid section offers detailed information on the phenotypes and biological functions related to the user-selected lipid. To begin your search, you must first select your target input. For lipid searching, enter the desired lipid name in the search box and click the submit button to initiate the search. Below are the two ways to search.

1. To search on the home page, follow these steps:
   1. Go to the home page.
   2. Select the "lipid" tab.
   3. Enter the common name, alias, abbreviation, LipidMaps ID, or MESH ID of the lipid you are looking for in the search box.
      Note: As you type in the search box, matching words will appear to assist you in finding the desired lipid.
   4. Click the "Submit" button to initiate the search.
   
   



2. To search on the lipid page, follow these steps:
   1. Go to the lipid page.
   2. Enter the common name, alias, abbreviation, LipidMaps ID, or MESH ID of the lipid you are looking for in the search box.
      Note: As you type in the search box, matching words will appear to assist you in finding the desired lipid.
   3. Click the "Submit" button to initiate the search.
   
   

After submitting, you can now access the search results, divided into three main sections: Target lipid, Phenotype Association, and Biological Function Association. Below is the summary and overview screenshot for each part. Further details will be provided in the following sections, corresponding to the numbered sections in the screenshots.

1. Target lipid: This section provides essential details about the selected lipid, including its basic information, external ID, Lipidmaps classification, string Representations, and the top five associated phenotypes and biological functions. It also includes up-stream and down-stream network graphs to understand this lipid better.
   
2. Lipid-phenotypes association: In this section, you can explore the connections between the user-selected lipid and its associated phenotypes. The results included a summary table, evidence table, phenotype network, inferred tree view, and word cloud.
   
3. Lipid-biological functions association: In this section, you can explore the connections between the user-selected lipid and its associated biological functions. The results included a summary table, evidence table, biological function network, inferred tree view, and word cloud.
   

The lipid section provides target lipid information, including basic information(synonyms, formula, abbreviation), external ID, lipidmaps classification, string representations, and top 5 associated-phenotypes and associated-biological functions.
Click on the linked word in the external ID, then you can direct to the related page of the database. For example, if you click the link of Lipidmaps, you will access the Lipidmaps page of the target lipid.

This section provides information about the upstream and downstream lipids of the target lipid. You can switch between the upstream and downstream graphs using the provided tabs. Below is a screenshot of the tabs, and the details of each graph will be described in the following sections, corresponding to the marked order in the screenshot.

1. The graph displays the upstream of the lipid. The graph's manipulation is provided below, corresponding to the order in the screenshot. You can manipulate the graph by clicking on the toolbar at the bottom right and left.
   
2. This graph visualizes the downstream of the lipid. The size of each node corresponds to the number of associated downstream lipid species. Nodes with a bold frame indicate the presence of downstream lipids, and you can click on them to expand their downstream lipids.
   For example, after you click on the node in the below screenshot, its downstream lipid will display.
   
   Note: The graph will not display if the target lipid has no downstream lipids.

This section consists of 5 subsections: a summary table, an evidence table, an associated-phenotypes network, an associated-phenotypes inferred tree view, and an associated-phenotypes word cloud. You can navigate through each subsection by switching the tabs. Below is a screenshot of the tabs, and the details of each subsection will be described in the following, corresponding to the number marked in the screenshot.

Below is the screenshot of the summary table section. The following descriptions will match the indicated order in the plot.

1. The first line of the description provides the total counts of associated phenotypes and publications mentioning the lipid-phenotypes association.
2. This table displays phenotypes associated with the target lipid, providing their names and the number of related lipids. Additional details include the count of literature references and the earliest and latest literature mentioning this association. Each column is explained below.
   • Phenotype name: The name of the phenotype related to the target lipid.
   • Associated lipids count: The total number of lipids associated with a specific phenotype.
   • Literature: The count of references containing sentences mentioning the target lipid and a specific phenotype.
   • Earliest publication year: The earliest literature reference year mentioned the association between the target lipid and a specific phenotype.
   • Last publication year: The most recent literature reference year mentioned the association between the target lipid and a specific phenotype.
   
   To better view the summary table, you can click on the column name to reorder it. For example, if you click on the column "Associated lipids count," the values will be displayed in ascending order based on the count of associated lipids.
   
   Furthermore, if you want to access the sentences that mention a specific lipid-phenotype association, click on the number in the "Literature" column. You will direct to the evidence table, which lists all the sentences extracted from literature references related to the specific lipid-phenotype association.
   
   

The evidence table provides the sentences extracted from literature references mentioning the target lipid and a specific phenotype. The table includes additional information such as each reference's PMID (PubMed ID), the count of literature references, whether the associations are under expert curation, and literature's publication year.

Each column is explained below:

• PMID: PubMed ID of the literature.
• Sentence: The sentence that mentions the target lipid and a specific phenotype. Phenotypes, lipids, and verbs are highlighted for clarity in each sentence as Phenotype, Lipid, and Verb. If a word is supposed to be highlighted by more than two colors, it will be displayed in grey.
• Literature: The count of references containing sentences mentioning the target lipid and a specific phenotype.
• Phenotype name: The name of the phenotype related to the target lipid.
• Expert curation: Expert curation status of the literature. If the lipid-phenotype association in the sentence is under expert curation, the value will be marked as "Yes"; otherwise, it will be marked as "No."
• Publication year: The year when the literature is published.

Furthermore, if you want to access the full article of a specific literature that mentions a lipid-phenotype association, click the link in the "PMID" column. You will direct to the corresponding page on PubMed for this literature.

The network visualizes phenotypes associated with the target lipid. Node sizes and colors represent the literature records documenting the lipid-phenotype association. Nodes without literature are marked white, while nodes with more literature records are red.
The network's manipulation is provided below, corresponding to the order in the screenshot.

1. Manipulate the network by clicking on the toolbar at the bottom right and left.
   
2. Explore the information of a specific colored node by hovering over a specific colored node to view its count of literature that mention this phenotype and target lipid.
   Furthermore, if you click on this node, you will access to the evidence table, which lists the sentences extracted from literature references that mention the target lipid and this phenotype.
   
   

The inferred tree visualizes phenotypes associated with the target lipid based on disease categories in MeSH (Medical Subject Headings). This tree displays the phenotypes into hierarchical relationships within different disease categories.

Node sizes indicate the total counts of downstream nodes' literature references. Each node's color is based on the literature count of the node itself. Nodes without literature are marked in white, while nodes with more literature records are near red. Nodes with a bold frame indicate the presence of downstream nodes.
The network's manipulation is provided below, corresponding to the order in the screenshot.

1. Click on the bold frame nodes to expand or collapse their associated downstream lipids.

2. Explore the information of a specific colored node.
   A colored node represents the association of this phenotype and the target lipid has been mentioned in more than a literature reference. You can hover over a specific colored node to view its count of literature that mention this phenotype and target lipid, and also total literature count of its downstream nodes.
   
   
   Furthermore, if you click on a colored node, a pop-up window will appear, asking whether you want to access the evidence table. The evidence table will list sentences from literature references mentioning the target lipid and this specific phenotype.
   Click "Yes" to direct to the evidence table containing all relevant sentences extracted from the literature for the selected node. Click "No" to remain on the current page.
   

The word cloud presents phenotypes associated with the target lipid. Phenotype names displayed in larger sizes represent more literature documenting this lipid-phenotype association. You can hover over a specific phenotype name to view the count of literature that mention this phenotype and target lipid.

Click on a specific phenotype name to access the evidence table listing all the relevant sentences from the literature for the association between the target lipid and that phenotype.
For instance, clicking on "Immunologic Deficiency Syndromes" will direct you to the evidence table for the target lipid and Immunologic Deficiency Syndromes association.

This section consists of 5 subsections: a summary table, an evidence table, an associated-biological functions network, an associated-biological functions inferred tree view, and an associated-biological functions word cloud. You can navigate through each subsection by switching the tabs. Below is a screenshot of the tabs, and the details of each subsection will be described in the following, corresponding to the number marked in the screenshot.

Below is the screenshot of the summary table section. The following descriptions will match the indicated order in the plot.

1. The first line of the description provides the total counts of associated biological functions and publications mentioning the lipid-biological functions association.
2. This table displays biological functions associated with the target lipid, providing their names and the number of related lipids. Additional details include the count of literature references and the earliest and latest literature mentioning this association.
   Each column is explained below.
   • Biological function name: The name of the biological function related to the target lipid.
   • Associated lipids count: The total number of lipids associated with a specific biological function.
   • Literature: The count of references containing sentences mentioning the target lipid and a specific biological function.
   • Earliest publication year: The earliest literature reference year mentioned the association between the target lipid and a specific biological function.
   • Last publication year: The most recent literature reference year mentioned the association between the target lipid and a specific biological function.
   
   To better view the summary table, you can click on the column name to reorder it. For example, if you click on the column "Associated lipids count," the values will be displayed in ascending order based on the count of associated lipids.
   
   
   Furthermore, if you want to access the sentences that mention a specific lipid-biological function association, click on the number in the "Literature" column. You will direct to the evidence table, which lists all the sentences extracted from literature references related to the specific lipid-biological function association.
   

The evidence table provides the sentences extracted from literature references mentioning the target lipid and a specific biological function. The table includes additional information such as each reference's PMID (PubMed ID), the count of literature references, whether the associations are under expert curation, and literature's publication year.

Each column is explained below:

• PMID: PubMed ID of the literature.
• Sentence: The sentence that mentions the target lipid and a specific biological function. Biological functions, lipids, and verbs are highlighted for clarity in each sentence as Biological function, Lipid, and Verb. If a word is supposed to be highlighted by more than two colors, it will be displayed in grey.
• Literature: The count of references containing sentences mentioning the target lipid and a specific biological function.
• Biological function name: The name of the biological function related to the target lipid.
• Expert curation: Expert curation status of the literature. If the lipid-biological function association in the sentence is under expert curation, the value will be marked as "Yes"; otherwise, it will be marked as "No."
• Publication year: The year when the literature is published.

If you want to access the full article of a specific literature that mentions a lipid-biological function association, click the link in the "PMID" column. You will direct to the corresponding page on PubMed for this literature.

The network visualizes biological functions associated with the target lipid. Node sizes and colors represent the literature records documenting the lipid-biological function association. Nodes without literature are marked white, while nodes with more literature records are red.
The network's manipulation is provided below, corresponding to the order in the screenshot.

1. Manipulate the network by clicking on the toolbar at the bottom right and left.
   
2. Explore the information of a specific colored node by hovering over a specific colored node to view its count of literature that mention this biological function and target lipid.
   Furthermore, if you click on this node, you will access to the evidence table, which lists the sentences extracted from literature references that mention the target lipid and this biological function.
   

The inferred tree visualizes lipids associated with the target biological function based on Lipidmaps and lipid classification structure in MeSH (Medical Subject Headings). Node sizes indicate the total counts of downstream nodes' literature references. Node sizes indicate the total counts of downstream nodes' literature references. Each node's color is based on the literature count of the node itself. Nodes without literature are marked in white, while nodes with more literature records are near red. Nodes with a bold frame indicate the presence of downstream nodes.
The network's manipulation is provided below, corresponding to the order in the screenshot.

1. Click on the bold frame nodes to expand or collapse their associated downstream lipids.

2. Explore the information of a specific colored node.
   A colored node represents the association of this biological function and the target lipid has been mentioned in more than a literature reference. You can hover over a specific colored node to view its count of literature that mention this biological function and target lipid, and also total literature count of its downstream nodes.
   
   
   Furthermore, if you click on a colored node, a pop-up window will appear, asking whether you want to access the evidence table. The evidence table will list sentences from literature references mentioning the target lipid and this specific biological function.
   Click "Yes" to direct to the evidence table containing all relevant sentences extracted from the literature for the selected node. Click "No" to remain on the current page.
   

The word cloud presents biological functions associated with the target lipid. Biological function names displayed in larger sizes represent more literature documenting this lipid-biological function association.
The wordcloud's manipulation is provided below.

1. Hover over a specific biological function name to view the count of literature that mention this biological function and target lipid.
   
2. Click on a specific biological function name to access the evidence table listing all the relevant sentences from the literature for the association between the target lipid and that biological function.
   For instance, clicking on "Signal Transduction" will direct you to the evidence table for the target lipid and Signal Transduction association.

The Phenotype section offers detailed information on lipids related to the user-selected phenotype. To begin your search, you must first select your target input. For phenotype searching, enter the desired phenotype name in the search box and click the submit button to initiate the search. Below are the two ways to search.

1. To search on the home page, follow these steps:
   1. Go to the home page.
   2. Select the "Phenotype" tab.
   3. Enter the common name, alias, or MESH ID of the phenotype you are looking for in the search box.
      Note: As you type in the search box, matching words will appear to assist you in finding the desired phenotype.
   4. Click the "Submit" button to initiate the search.
   


2. To search on the phenotype page, follow these steps:
   1. Go to the phenotype page.
   2. Enter the common name, alias, or MESH ID of the phenotype you are looking for in the search box.
      Note: As you type in the search box, matching words will appear to assist you in finding the desired phenotype.
   3. Click the "Submit" button to initiate the search.
   

After submitting, you can now access the search results. This results consists of 5 sections: a summary table, an evidence table, an associated-lipids network, an associated-lipids inferred tree view, and an associated-lipids word cloud. You can navigate through each section by switching the tabs. Below is a screenshot of the tabs, and the details of each section will be described in the following, corresponding to the number marked in the screenshot.

This section lists the information of the target phenotype, including its name, description, MeSH ID, and top 5 Associated lipids.


You can click on the MeSH ID link to access the corresponding page of MeSH for this phenotype.

Below is the screenshot of the summary table section. The following descriptions will match the indicated order in the plot.

1. The first line of the description provides the total counts of associated lipids and publications mentioning the phenotype-lipids association.
2. This table below the information box displays lipids associated with the target phenotype, providing their names and the number of related lipids. Additional details include the count of literature references and the earliest and latest literature mentioning this association. Each column is explained below.
   • Lipid name: The name of the Lipid related to the target phenotype.
   • Associated phenotypes count: The total number of phenotypes associated with a specific lipid.
   • Literature: The count of references containing sentences mentioning the target phenotype and a specific lipid.
   • Earliest publication year: The earliest literature reference year mentioned the association between the target phenotype and a specific lipid.
   • Last publication year: The most recent literature reference year mentioned the association between the target phenotype and a specific lipid.
   
   To better view the summary table, you can click on the column name to reorder it. For example, if you click on the column "Associated phenotypes count," the values will be displayed in ascending order based on the count of associated phenotypes.
   
   
   Furthermore, if you want to access the sentences that mention a specific phenotype-lipid association, click on the number in the "Literature" column. You will direct to the evidence table, which lists all the sentences extracted from literature references related to the specific phenotype-lipid association.
   

The evidence table below the information box provides the sentences extracted from literature references mentioning the target phenotype and a specific lipid. The table includes additional information such as each reference's PMID (PubMed ID), the count of literature references, specificity index, pleiotropy index, whether the associations are under expert curation, and literature's publication year.
Each column is explained below:

• PMID: PubMed ID of the literature.
• Sentence: The sentence that mentions the target phenotype and a specific lipid. Phenotypes, lipids, and verbs are highlighted for clarity in each sentence as Phenotype, Lipid, and Verb. If a word is supposed to be highlighted by more than two colors, it will be displayed in grey.
• Literature: The count of references containing sentences mentioning the target phenotype and a specific lipid.
• Specificity index: Specificity index values.
• Pleiotropy index: Pleiotropy index values.
• Expert curation: Expert curation status of the literature. If the phenotype-lipid association in the sentence is under expert curation, the value will be marked as "Yes"; otherwise, it will be marked as "No."
• Publication year: The year when the literature is published.

Furthermore, if you want to access the full article of a specific literature that mentions a phenotype-lipid association, click the link in the "PMID" column. You will direct to the corresponding page on PubMed for this literature.

The network visualizes lipids associated with the target phenotype. Node sizes and colors represent the literature records documenting the phenotype-lipids association. Nodes without literature are marked white, while nodes with more literature records are red.
The network's manipulation is provided below, corresponding to the order in the screenshot.

1. Manipulate the network by clicking on the toolbar at the bottom right and left.
   
2. Explore the information of a specific colored node.
   You can hover over a specific colored node to view two values.
   • Literature from downstream lipid species: The count of literature that mentions downstream lipid species (of this node) and the target phenotype.
   • Node literature: Count of literature that mention this lipid (node) and target phenotype.
   
   Furthermore, if you click on this node, you will access to the evidence table, which lists the sentences extracted from literature references that mention the target phenotype and this lipid.
   

The inferred tree visualizes lipids associated with the target phenotype based on Lipidmaps and lipid classification structure in MeSH (Medical Subject Headings). Node sizes indicate the total counts of downstream nodes' literature references. Each node's color is based on the literature count of the node itself. Nodes without literature are marked in white, while nodes with more literature records are near red. Nodes with a bold frame indicate the presence of downstream nodes.
The network's manipulation is provided below.

1. Click on the bold frame nodes to expand or collapse their associated downstream lipids.

2. Explore the information of a specific colored node.
   A colored node represents the association of this lipid and the target phenotype has been mentioned in more than a literature reference. You can hover over a specific colored node to view its count of literature that mention this lipid and target phenotype, and also total literature count of its downstream nodes.
   
   Furthermore, if you click on a colored node, a pop-up window will appear, asking whether you want to access the evidence table. The evidence table will list sentences from literature references mentioning the target phenotype and this specific lipid.
   Click "Yes" to direct to the evidence table containing all relevant sentences extracted from the literature for the selected node. Click "No" to remain on the current page.
   

The word cloud presents lipids associated with the target phenotype. Lipid names displayed in larger sizes represent more literature documenting this phenotype-lipid association.
The wordcloud's manipulation is provided below, corresponding to the order in the screenshot.

1. Hover over a specific lipid name to view the count of literature that mention this lipid and target phenotype.
   
2. Click on a specific lipid name to access the evidence table listing all the relevant sentences from the literature for the association between the target phenotype and that lipid.
   For instance, clicking on "Ceramides" will direct you to the evidence table for the target phenotype and Ceramides association.

Below is the screenshot of the phenotype-lipids correlation. The following descriptions will match the indicated order in the plot.

1. The bar plot displays the top 10 associated biological functions based on the correlation coefficient. The x-axis shows biological function names, and the y-axis shows correlation coefficient values.
2. The Sankey diagram illustrates how the targeted phenotype is associated with lipids and biological functions. The connecting lines between nodes represent the associations, with thicker lines indicating stronger associations.

The Biological function section offers detailed information on lipids related to the user-selected biological function. To begin your search, you must first select your target input. For biological function searching, enter the desired biological function name in the search box and click the submit button to initiate the search. Below are the two ways to search.

1. To search on the home page, follow these steps:
   1. Go to the home page.
   2. Select the "Biological function" tab.
   3. Enter the common name, alias, or MESH ID of the biological function you are looking for in the search box.
      Note: As you type in the search box, matching words will appear to assist you in finding the desired biological function.
   4. Click the "Submit" button to initiate the search.
   
2. To search on the Biological function page, follow these steps:
   1. Go to the Biological function page.
   2. Enter the common name, alias, or MESH ID of the biological function you are looking for in the search box.
      Note: As you type in the search box, matching words will appear to assist you in finding the desired biological function.
   3. Click the "Submit" button to initiate the search.
   

After submitting, you can now access the search results. This results consists of 5 sections: a summary table, an evidence table, an associated-lipids network, an associated-lipids inferred tree view, and an associated-lipids word cloud. You can navigate through each section by switching the tabs. Below is a screenshot of the tabs, and the details of each section will be described in the following, corresponding to the number marked in the screenshot.

This section lists the information of the target biological function, including its name, synonyms, description, MeSH ID, and top 5 Associated lipids.


You can click on the MeSH ID link to access the corresponding page of MeSH for this biological function.

Below is the screenshot of the summary table section. The following descriptions will match the indicated order in the plot.

1. The first line of the description provides the total counts of associated lipids and publications mentioning the biological function-lipids association.
2. This table below the information box displays lipids associated with the target biological function, providing their names and the number of related lipids. Additional details include the count of literature references and the earliest and latest literature mentioning this association.
   Each column is explained below.
   
   • Lipid name: The name of the Lipid related to the target biological function.
   • Associated biological functions count: The total number of biological functions associated with a specific lipid.
   • Literature: The count of references containing sentences mentioning the target biological function and a specific lipid.
   • Earliest publication year: The earliest literature reference year mentioned the association between the target biological function and a specific lipid.
   • Last publication year: The most recent literature reference year mentioned the association between the target biological function and a specific lipid.
   
   To better view the summary table, you can click on the column name to reorder it. For example, if you click on the column "Associated biological functions count," the values will be displayed in ascending order based on the count of associated biological functions.
   
   Furthermore, if you want to access the sentences that mention a specific biological function-lipid association, click on the number in the "Literature" column. You will direct to the evidence table, which lists all the sentences extracted from literature references related to the specific biological function-lipid association.
   

The evidence table provides the sentences extracted from literature references mentioning the target biological function and a specific lipid. The table includes additional information such as each reference's PMID (PubMed ID), the count of literature references, specificity index, pleiotropy index, whether the associations are under expert curation, and literature's publication year.
Each column is explained below:

• PMID: PubMed ID of the literature.
• Sentence: The sentence that mentions the target biological function and a specific lipid. Biological functions, lipids, and verbs are highlighted for clarity in each sentence as Biological function, Lipid, and Verb. If a word is supposed to be highlighted by more than two colors, it will be displayed in grey.
• Literature: The count of references containing sentences mentioning the target biological function and a specific lipid.
• Specificity index: Specificity index values.
• Pleiotropy index: Pleiotropy index values.
• Expert curation: Expert curation status of the literature. If the biological function-lipid association in the sentence is under expert curation, the value will be marked as "Yes"; otherwise, it will be marked as "No."
• Publication year: The year when the literature is published.

Furthermore, if you want to access the full article of a specific literature that mentions a biological function-lipid association, click the link in the "PMID" column. You will direct to the corresponding page on PubMed for this literature.

The network visualizes lipids associated with the target biological function. Node sizes and colors represent the literature records documenting the biological function-lipids association. Nodes without literature are marked white, while nodes with more literature records are red.
The network's manipulation is provided below, corresponding to the order in the screenshot.

1. Manipulate the network by clicking on the toolbar at the bottom right and left.

2. Explore the information of a specific colored node.
   You can hover over a specific colored node to view two values.
   • Literature from downstream lipid species: The count of literature that mentions downstream lipid species (of this node) and the target biological function.
   • Node literature: Count of literature that mention this lipid (node) and target biological function.
   
   Furthermore, if you click on this node, you will access to the evidence table, which lists the sentences extracted from literature references that mention the target biological function and this lipid.
   

The inferred tree below the information box visualizes lipids associated with the target biological function based on Lipidmaps and lipid classification structure in MeSH (Medical Subject Headings). Node sizes indicate the total counts of downstream nodes' literature references. Each node's color is based on the literature count of the node itself. Nodes without literature are marked in white, while nodes with more literature records are near red. Nodes with a bold frame indicate the presence of downstream nodes.
The network's manipulation is provided below.

1. Click on the bold frame nodes to expand or collapse their associated downstream lipids.


2. Explore the information of a specific colored node.
   A colored node represents the association of this lipid and the target biological function has been mentioned in more than a literature reference. You can hover over a specific colored node to view its count of literature that mention this lipid and target biological function, and also total literature count of its downstream nodes.
   
   
   Furthermore, if you click on a colored node, a pop-up window will appear, asking whether you want to access the evidence table. The evidence table will list sentences from literature references mentioning the target biological function and this specific lipid.
   Click "Yes" to direct to the evidence table containing all relevant sentences extracted from the literature for the selected node. Click "No" to remain on the current page.
   

The word cloud presents lipids associated with the target biological function. Lipid names displayed in larger sizes represent more literature documenting this biological function-lipid association.
The wordcloud's manipulation is provided below.

1. Hover over a specific lipid name to view the count of literature that mention this lipid and target biological function.
2. Click on a specific lipid name to access the evidence table listing all the relevant sentences from the literature for the association between the target biological function and that lipid.
   For instance, clicking on "Palmitic acid" will direct you to the evidence table for the target biological function and Palmitic acid association.

Below is the screenshot of the Biological function-lipids correlation. The following descriptions will match the indicated order in the plot.

1. The bar plot displays the top 10 associated phenotypess based on the correlation coefficient. The x-axis shows phenotype names, and the y-axis shows correlation coefficient values.
2. The Sankey diagram illustrates how the targeted biological function is associated with lipids and phenotypes. The connecting lines between nodes represent the associations, with thicker lines indicating stronger associations.