PubPharm help

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What is PubPharm?

  • PubPharm is a freely accessible, drug-centred search platform and the central service of the FID Pharmazie.
  • PubPharm offers more than 60 million citations, of which over 36 million are from the Medline database (PubMed). Additionally, PubPharm contains pharmaceutical, chemical and technological journals, preprints from various archives (bioRxiv, medRxiv, ChemRxiv, arXiv, engrXiv, Preprints. org, TechRxiv and ResearchSquare), books (e-books), international dissertations, conference proceedings, information on clinical trials from the ClinicalTrials.gov registry and the WHO International Clinical Trials Registry Platform, as well as a subject-specific selection of patents from the European Patent Office.
  • Pharmaceutical journals licensed (purchased) by the FID Pharmazie are available to authorised users. Resources from Medline are updated daily. References from other sources are updated at varying intervals from daily to monthly.
  • PubPharm contains innovative search tools that provide novel access paths to pharmacy-relevant information resources.

What are the technical details behind PubPharm?

Architecture of PubPharm

PubPharm is a discovery system based on the open-source software Qcovery/VuFind. These systems are modern library catalogues based on search engine technology. The data is integrated into a single search index. The aim of the Qcovery network is to provide a discovery system that can be easily adapted to different use cases so that the adaptation effort through programming is reduced. The backend, i.e. the central search index K10plus-Zentral, is located at the Head Office of the GBV Common Library Network in Göttingen. The PubPharm architecture can be divided into three layers: data sources, data management and frontend.

  • Data sources: PubPharm relies on bibliographic data as the basis of the search and norm data (from the DrugBank database and the Medical Subject Headings) for search support, e.g., for generating search suggestions.
  • Data management: The data from the various sources are transferred to an index (Apache Solr Cloud) via the infrastructure of the Head Office of the GBV Common Library Network. The data sources include, among others, the metadata of the biomedical database Medline (PubMed), pharmacy and chemistry collections of the Braunschweig University Library, study registers, preprint archives and journals licensed by the FID Pharmazie. Therefore, a query in PubPharm can identify matching journal articles, preprints, clinical studies and books or dissertations (from collections of most German university libraries and international dissertations), which reduces the need for individual searches in several databases.
  • Frontend: The search platform is based on the open-source software Qcovery/VuFind and can be accessed via the new PubPharm portal (based on TYPO3). All other services (e.g., social media channels) are also integrated into this portal.

Full-text access

  • The search index contains metadata on each record. It provides information such as title, author(s), year of publication, document type. Metadata do not (usually) contain full texts. For electronic sources (e-books, e-articles), a link to the full text is often listed in the metadata, or information is provided which can be used to generate such a link in the result list. Access to the full text depends on many factors, such as whether it is open access or licensed by the local institution (see next section).
  • Sometimes, the metadata do not contain information on the full-text link. In these cases, you can navigate via the journal homepage, volume and issue to get to the desired article.

 

Availability check

  • PubPharm displays whether free full-text access is available depending on the individual location. An availability check based on the IP address of the search query is used for this purpose.
  • The availability check proceeds stepwise. In the initial step, it is determined whether the publication is open access or freely accessible. In the next step, the local license for the source is checked. A link resolver is used to determine the IP authorisation for IP addresses belonging to German, Austrian or Swiss universities. It is important to be in your university network to access full-text versions. If this is not the case, it is recommended to prove whether your university offers a VPN service. The next step is to check whether the hit has been licensed by the FID Pharmazie (FID-licences). If direct full-text access is not possible, a link to the commercial document delivery service "subito" (https://www.subito-doc.de/) is offered (if available). Alternatively, a request can be sent to the FID Pharmazie. The FID Pharmazie will then determine whether and how access to the full text is possible.

How can I search more specifically?

Search operators

  • Standard search
    A standard search looks for the search term and for similar terms with the same word stem (based on Porter Snowball).
  • Search with wildcards (truncation or wildcards)
    When searching, a * can be used as a wildcard for any number of characters, at any position or at the end of a word. It cannot be used as the very first character of a term. In principle, a search is performed for search terms that share the same word beginning. For example, the output of a search for hyperic* contains results with hypericum, hypericin or hypericaceae. If a ? is used as a wildcard at any position or at the end of a word, it stands for exactly one character. A ? cannot be used as a placeholder directly at the beginning of a word.
  • Exact word or phrase search using quotation marks
    The phrase search "..." searches for the specified word sequence. Wildcards/truncation (*, ?) within quotation marks are not supported. In these cases, a search for * or ? is conducted. A phrase search can be used, e.g., if search terms are to appear immediately after the other ("capillary electrophoresis", "chiral separation"). The phrase search is also helpful if searching for authors: "Steinhilber, Dieter" OR "Steinhilber, D".
  • Use of word spacing operators/proximity search
    A word distance search can be triggered by adding a tilde (~) and a numeric value to the search phrase. For example, to search for "meta" and "analysis" within a maximum distance of two words between them, enter this search query: "meta analysis"~2.

 

Combination of search terms (Boolean operators)
Boolean operators make it possible to combine search terms. For example, it is possible to search for titles containing several search terms, either one or the other search term, or one search term and not another. The use of parentheses allows search queries to be refined to fit. The following is an explanation of each operator:

  • AND
    The AND operator (logical AND) is used by default, when no operator is placed between two words. If you combine terms with AND, you will get hits in which all search words are present. Example: You search for titles containing the words hot and melt and extrusion: hot melt extrusion corresponds to hot AND melt AND extrusion.
  • OR
    If there is a logical OR between two words, you will get hits in which one or both words are found. Example: You search for titles containing the terms aspirin or warfarin: aspirin OR warfarin.
  • NOT or -
    You can use the NOT operator to exclude hits that contain this word. Example: You want to search for titles containing hypericum but not perforatum: hypericum NOT perforatum. You will get the same result with hypericum -perforatum.

 

Use of parentheses
For more complex queries, the use of parentheses is helpful to group search terms and operators. For example, you are searching for publications that contain the phrases (see Exact word or phrase search using quotation marks) "vitamin c" or "ascorbic acid" and at the same time encapsulation, microencapsulation, microsphere: ("vitamin c" OR "ascorbic acid") AND (encapsulation OR microencapsulation OR microsphere). It is important to use parentheses in such complex searches and to insert an operator between all search terms. If NOT, - or OR are used somewhere in the search query, search terms between which there is no operator will be connected with an AND during the search. Furthermore, the advanced search in PubPharm can be used for structured input of more complex queries. Queries are limited to a maximum of 500 characters in the central input line.

How can I sort and limit the number of results?

Refine the search by narrowing and sorting the results (see arrow 1)

  • Change sort order
    By default search results are sorted by publication date (newest hits first). Sorting by relevance (most relevant article first), oldest hits first, author (in alphabetically ascending order) or journal title is also possible (see arrow 2). The number of displayed hits on a page can be expanded from 10 to 20 or 50 hits.
  • Sorting by relevance
    Sorting by relevance is made possible by a specialised algorithm. High weighting is given to topics (keywords), the main author and the title. Low weighting has, e.g., full text, the publisher, ISBN and ISSN.

Filter functions
A large number of results can be refined by different filters, e.g., for media type, journal title, year of publication, subject or language (see arrow 4). Furthermore, checkbox filters are offered to restrict the search to clinical trials (yes/no) from the ClinicalTrials.gov registry and the International Clinical Trials Registry Platform (ICTRP) of the WHO, patents (yes/no), systematic reviews (yes/no) and current publications with a focus on COVID-19/SARS-CoV-2 (see arrow 3). Using the filter "Systematic Reviews", hits are obtained that have "systematic" and "review" in their title. Via additional checkbox filters, systematic reviews, clinical trials, and patents can be excluded from the result list. The different filters can be (logically) combined with each other and are linked with a logical AND.
Searches and filter settings can be recalled in the search history and saved in the personal account (see How can I use the list of favourites and the export function?).

What information can I find in the result list?

You can see by means of the icon which source is listed (e.g., journal article, see arrow 1). In addition, the title, further information on the respective source (e.g., journal title, year of publication, etc.), the first three authors and the result of the availability check (full-text availability, see also What are the technical details behind PubPharm?) are displayed.

In addition, information on citation statistics and the social media impact of the source provided by the Dimensions database and Altmetric is linked (see arrow 2 and arrow 3). These data are available for each source in PubPharm that has a digital object identifier (DOI) and has been cited or mentioned in social media at least once. With each new search, the citation information is dynamically queried from the respective provider and is thus up-to-date on a daily basis. Clicking the Dimensions citation icon will take you to their webpage listing the citing articles. Altmetric provides information on the social media resonance of the searched article.

What information do I find in the detailed view?

In the detailed view, you will find information about the respective result. If available in the data set, you find in all the sources:

  • An abstract or outline of objectives, results, and conclusions
  • A list of all authors
  • Under "Keywords", keywords are listed for the respective result.
  • Information about the result, e.g., ISSN/ISBN numbers, year of publication, DOI, and information about the source/copyright.

Depending on the data source, you will also find additional information in the detailed view:

Journal article

  • Under "Access & Availability" and "Links", you may find several links to the full text. The site-dependent availability is indicated there in each case.

Journal title

  • Under "Associated Publications/Volumes", you will find all articles published in the journal.

Book / E-Book

  • For e-books, you may find several links to the full text under "Access & Availability".
  • For books and e-books that are not open access, there is no site-specific availability check.
  • Under "Links", there is often a link to the table of contents.

Clinical studies

  • For each clinical trial, the entry in PubPharm contains the title and short title of the study, a brief study description if available, the study phase and status, and identification numbers. The entire entry in the study register can be accessed via the direct link under "Access & Availability".

Patents

  • Under "Keywords", you will find information on the patent classification and under "Patent number" the identification number(s). Via the direct link under "Access & Availability", the entire entry can be viewed on the page of the European Patent Office.

 

Why is there often not only one link to the full text in the detail view but several?
In the detailed view, all links are displayed that are listed in the metadata for the respective entry. The location-dependent availability is marked in each case. Depending on which user group you belong to, different links may be of interest (for more information, see section How do I get the full text of a source?).

How do I get the full text of a source?

In the result list, the availability check shows you whether the full text of a source is directly available (free of charge) (see What are the technical details behind PubPharm?) The availability check is based on the IP address of the search query and thus enables the display of full-text access options at the respective location.

The direct link to the full text is displayed, if available. In some cases, only a link to the journal page is displayed, and the desired article can be searched by year, issue, etc. on the journal page. In the table, you will find an overview of the various access options that are displayed in PubPharm:

LinkDescription
Free full-text access (direct link)Full text is directly (freely) accessible.
Check full-text access (link to provider)There is a link to the full text, but it is (probably) not accessible free of charge. The accessibility option should be checked, though.
Check possibility for subito orderThere is no link to the full text, however, the source would be available through the commercial document delivery service "subito".
No direct access to publication possible - Send inquiry to PubPharm-TeamIt is a print version of a book or an article, which may not be available at your local library. Another reason could be the absence of a direct link to the full text. For availability information, please contact the PubPharm team.
Library // location abbreviation (print version available in your institution)Besides the electronic availability check, PubPharm searches for printed copies of the sources that ideally are located at your local library. If there is a local print copy available, further information is provided.

What can I do if I need the full text of a journal article, but it is not directly accessible?

  • If you have the possibility to do so, it is worthwhile to dial in via the IP network of a German university (e.g., via VPN). The availability is checked depending on the location (based on the IP address). The desired source could be licensed by your university library and is therefore available for you.
  • It is worth looking for the journal containing the desired article in the local library catalogue as a print version. If the journal is not available at your own location, the article can be ordered via interlibrary loan from the local library. Alternatively, the full text, if available, can be ordered via the commercial document delivery service "subito".
  • The detailed view of a result often contains several links. It is worthwhile to check these. When querying availability, not all links can be examined for technical reasons. However, it is possible that one of the other links given provides free access to the full text.
  • It may be worthwhile to search for the title of the desired article in another search engine, e.g., Google Scholar. The full texts are sometimes freely available through institutional repositories or social networks.
  • The FID Pharmazie can help with full-text access to print versions of all articles included in PubPharm. Please send a request to pubpharm [at] tu-braunschweig.de.

What can I do if I need the full text of a book (print or e-book) or a printed journal article?

  • The availability check is not done for printed books. For e-books, only open access availability is checked. This means it is worth looking for the desired book in the local library catalogue. If the book is not available there, it can be ordered via interlibrary loan from the local library. Alternatively, the book or partial copies, if available, can be ordered through the commercial document delivery service "subito".
  • For printed journal articles, it is worthwhile to search for the journal containing the desired article in the local library catalogue. If the journal is not available at one's own location, the article can be ordered via interlibrary loan from the local library. Alternatively, the full text, if available, can be ordered via the document delivery service "subito".

How can I use the list of favourites and the export function?

Favourites lists

  • By clicking the favourites button (star, see arrow 1), individual results can be added to the favourites list (see arrow 2). From this list, it is possible to export all or selected titles, print them, send them as a link list by email or save them in a permanent list in the user account (free account) (see arrow 3).
  • You can basically create favourites lists in a browser session without logging in. A personal account is required to save and later edit these lists.

Personal account

  • You can create a free personal account to save watch lists (favourites lists) and search queries via the search history.
  • The account can be created under "My Account" and "Create New Account" (see arrow 1 and arrow 2).
  • Entries in the favourites list can be transferred to a new or existing list via "Save". Hits of a list can be sorted by "Title", "Author", "Newest first" and "Oldest first".
  • Selected entries of a list can be sent by email or exported for, e.g., a literature management program.

What can I use the export function for?

  • Results can be exported, e.g., for a literature management program (e.g., Citavi, EndNote, Mendeley or Zotero) (see arrow 1). A literature management program or reference manager contains a database into which (meta) data of publications can be imported and managed. The link to a word processing program makes it possible to insert references and literature lists in a citation style.
  • BibTex, EndNote, EndNoteWeb, RefWorks, MARC, MARCXML and RIS are offered as export formats. In addition for each result, a corresponding ID, such as DOI and COinS, are offered in the interface for browser extensions of reference management tools.

How can I be automatically notified about newly indexed hits?

  • An RSS feed for a search query can be called up and subscribed below the result list (see arrow 2). The feed shows newly added entries with the title and year of publication. To read the RSS feed, you need a so-called feed reader. These tools are available free of charge.

How can I use the advanced search?

The advanced search can be used for more selective and complex queries (see arrow 1). It can be defined which index fields (metadata) for which search term should be searched (see arrow 4). For example, you can search for all publications of an author in a specific journal.

A video tutorial is available to introduce the advanced search (see arrow 6).

The following index fields can be selected in the advanced search:

  • Standard search: Search in fields with main contents: Author(s), title, keywords, abstract, table of contents, publisher, ISBN/ISSN.
  • Title: Search within the title (e.g., titles of articles and books).
  • Journal Title: Search within the title of journals. Articles published in the particular journal will also be returned.
  • Person: Search for authors (including co-authors and other contributors).
  • Publisher: Search for the publisher (for books and journals).
  • Topic: It searches for publications on a specific topic. Each article in PubPharm is automatically assigned to specific topics that result from phrases and keywords. These words are available as part of the metadata for the selected article. In most cases, vocabulary words are used (such as Medical Subject Headings, MeSH). All data records from the Medline database in the search index should be provided with corresponding entries from MeSH. Other records may also contain both controlled vocabulary entries and free keywords.
  • Full text: The search term is searched in the full text. It should be noted, that full texts are not available in the database for all publications.
  • Table of contents: Search within the table of contents.
  • ISBN/ISSN: Search for the ISBN of books or ISSN of journals.
  • Year(s) of publication: Search for the publication year.
  • Index (all fields): In addition to the standard search, additional fields, such as URL, are parsed. This search function provides the most comprehensive search.

Search Fields

Within the search fields (see arrow 2 and arrow 3), you can combine search words with the operators and search functions supported by PubPharm (see How can I search more specifically?). All search fields of a search group can be combined with boolean operators.

  • AND Returns only the hits that contain all words or phrases from this search group.
  • OR Returns the hits that contain one word or all words or phrases from this search group.
  • NOT Returns all hits that contain words or phrases not specified in this search group. This search condition works only when searching in at least two search fields.

Search Groups

Some search queries are more complicated, and searching across different fields is not enough. With search groups you can group search fields: You can use "AND" or "OR" to link the search groups (see arrow 5).

Example

You want to search for titles on bisoprolol and captopril for the treatment of hypertension:

  • Add the terms "bisoprolol" and "hypertension" to the input fields of the first search group and leave the "search operator" for the group set to "AND".
  • Add another search group and enter the terms "captopril" and "hypertension" there, and leave the "search operator" for the group on "AND".
  • Set the search operator for the combination of search groups to "OR".

How to search with search commands?

Search commands can be used in the search query to specify which index fields should be searched for which search term (see How can I use the advanced search?). The following search commands can be used in PubPharm:

CommandDescriptionExample
ALLSearch term is searched in all major search fields. This corresponds to the standard search. It is only needed as a search command if another search command is used simultaneously.ALL Diabetes
TITSearch term is searched in title, alternative title, previous and successor titles.TIT Diabetes
JTIFor journals, search term is searched in the journal title, and for articles belonging to a particular journal (in the journal reference), the search term is searched in the title of the related articles.JTI Diabetes
PERSearch term is searched for in the names of persons involved in the resource creation.PER Mustermann, Max
PUBSearch term is searched in the name of the publisher or the publishing institution.PUB Springer
THMSearch term is searched in fields containing topics, keywords and classifications.THM Diabetes
TXTSearch term is searched in full text, if available in the search index. Here the coverage is not very high and this search command is considered to be experimental.TXT Diabetes
TOCSearch term is searched in the table of contents.TOC Diabetes
ISNSearch term is searched in ISSN and ISBN.ISN 1234-5678
ERJSearch term is searched in the index field for the publication year.ERJ 2019
INDSearch term is searched in all fields available in the index.IND Diabetes

What does the structure search offer?

The structure search complements the text-based search as a unique function of PubPharm. It is based on data from the PubChem database. More information can be found in this section under Background information: What is behind the structure search?

For an introduction to the structure search, a video tutorial is available.

In the structure search, chemical compounds can be searched via a structure editor based on their molecular structure, via the international non-proprietary name or via import of SMILES/InChI code. Furthermore, substructure and similarity searches are possible starting from an identified substance. Various links (e.g., to PubChem and the DrugBank database) can be used to obtain further (drug) information. For an identified substance, publications can be searched in PubPharm.

Start the search

The following search options are available:

  • Draw a compound in the editor and search with "Search by Structure". Information about the editor can be found on the help page of the open-source Epam Ketcher used in PubPharm.
  • Enter the name of a substance and start the search with "Search by Name". The identified compound will be loaded into the editor and can be modified there if necessary.
  • Enter the InChI or SMILES code of a compound and start the search with "Import Structure". The structure is loaded into the editor and can be edited if necessary.

Result visualisation

If the compound is identified in the database, a short overview is displayed. The result contains information from PubChem and, if available, a short description from DrugBank. In addition, links to the entries in PubChem, DrugBank and the ChEMBL database (if available), as well as to the search interface of the European Patent Office are displayed for each result. "Search in PubPharm" can be used to search directly in PubPharm for publications on the substance, whereby the first 5 synonyms from PubChem are included in the search.

Further search options

Starting from an identified compound, the structure search can be continued:

  • Substructure search: compounds are searched that contain the substance as a substructure.
  • Similarity search: A search for structurally similar compounds is performed.

The search results are displayed as a list. Each result can be used again as a starting compound for new searches. Via "Load into Editor" the structure can be loaded into the editor and modified there.

If a structure was entered in the editor for which no matching substance is available in the PubChem database, the hit is marked with "?". Based on this compound, a substructure or similarity search can be performed.

Background info: What is behind the structure search?

The structure search is based on data and open-source tools of the PubChem database. The search results are determined and prepared for display via the PUG REST API. The substance search (based on the structure or name search) and substructure and similarity searches are performed via the PubChem PUG REST API. The PubChem search parameters and, where necessary, PubChem fingerprints are used.

What does the innovative suggestion functionality offer?

When searching for active substances and diseases/symptoms, suggestion lists of context-similar "related substances", "related diseases" and "related genes" are generated if available (i.e. a certain number of references must be available). For example, when searching for the inhibitor of dipeptidyl peptidase-4 sitagliptin, other drugs used to treat diabetes mellitus, e.g., metformin and exenatide, are listed among the related substances. Another example is the listing of kinase inhibitors when searching for vemurafenib in PubPharm. Further information can be obtained via links to the UniProt and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. In addition, the search can be continued in the structure search, the Drug Overviews or in the Narrative Service, depending on the information required.
This suggestion function was developed by the Institute of Information Systems and is based on machine learning technologies (further information). Text mining processes are used to link bioactive compounds with corresponding diseases and genes. The number of scientific publications linking active substances, diseases and genes is counted. The most frequent associations are displayed in the suggestion lists. A click on "Drug Overviews" or "Narrative Service" leads to a targeted search for this literature.

What does the Narrative Service offer?

The Narrative Service (a unique PubPharm characteristic) enables a precise and structured literature search by defining the relationships between different pharmaceutical concepts (e.g., active ingredients, dosage forms, plant families, targets, (laboratory) methods, etc.) in the search query. To do this, enter your information need (research question) as a subject-predicate-object relationship in the central input line. In addition, structured literature overviews can be generated using variables on pharmaceutically relevant concepts instead of concrete subjects or objects.

Various video tutorials are available as an introduction to the Narrative Service. More information can be found here.

Searching in the Narrative Service

Query Builder

  • Step 1: As the first step, the query must be formulated. The Narrative Service enables the targeted search for interactions between pharmaceutical concepts such as active substances, diseases and targets. The concepts (here metformin and disease) must be entered in the input mask (see arrow 1), which is supported by corresponding suggestions (auto-completion). You can also get an overview of the concepts and variables/placeholders via the "Browse" button. Afterwards, the interaction you are looking for (here treats) must be selected.
  • Step 2: You can start the search by clicking "Search" (see arrow 2). Alternatively, you can add the desired interaction to the current query via "Add". All interactions must be present in the corresponding document hits (logical AND).  
  • Step 3: After a successful search, you can view the results (see arrow 3). In the example search, the search was for diseases that are treated with metformin. In this case, the answer is a nested list: 4546 documents deal with the treatment of diabetes mellitus and 4118 with the treatment of diabetes mellitus type 2. By clicking on such a group, the individual results can be viewed.
    An important note: All displayed associations were automatically extracted from the literature. Unfortunately, possible incorrect extractions cannot be excluded.
  • Step 4: If a document appears to be particularly relevant, you can click on the coloured graph to display the content of the document (see arrow 4). The Narrative Service then visualises the title, abstract, authors and other metadata. Detected concepts are highlighted in colour in the texts, giving you a quick overview of the content. On the right-hand side, a graph structure is visualised that shows interactions between concepts that can be extracted from the corresponding document. With a click on the document ID, you are redirected to PubPharm. Another function is the so-called "Provenance" button. A click on this button shows you the text passage from the corresponding document that supports the searched interaction.
  • Step 5: The Narrative Service has various filter functions (see arrow 5). For example, the results can be limited to the date of publication. You can also use a free text field to filter the document hits by searching for word phrases in the titles. For example, entering child and pressing the enter key would limit the results to documents that contain "child" as a phrase in the title.

 

Keyword Search

If the interaction between search words is still unclear, a search can alternatively be started via "Keyword Search". With this search option, the pharmaceutical concepts (e.g., active ingredients, diseases and targets) can be entered in the input mask without selecting a predicate. Each concept (search word) is entered individually and confirmed with the Enter key or the "Add" button. After "clicking" on "Search", possible interaction patterns with different predicates are suggested. "Clicking" on the desired interaction pattern starts the literature search.

Below you can see an example search with the concepts metformin and diabetes mellitus.

What does the service Drug Overviews offer?

The Drug Overviews service (a unique PubPharm characteristic) is an extension of the Narrative Service. In this service, you can search specifically for an active substance and receive (I) existing information from the ChEMBL database (including pkA and logP values, molecular mass, etc.) and (II) extracted associations from the literature (including interactions with other active substances, information on targets and laboratory methods as well as indications and dosage forms).

An introduction to the Drug Overviews is available here (video tutorial). Information on the respective active substance is also visualised in the Drug Overviews in network views. A video tutorial introducing this feature is available here. More information on the Drug Overviews can be found here.

Searching in the Drug Overviews

Step 1: The Drug Overviews are substance-centred overviews generated from the current research literature. To start a search, enter a desired active substance in the input mask (see arrow 1). An auto-completion supports your input.

Step 2: Review of the fact sheet. The Drug Overviews first summarise known properties of an active substance such as the molecular formula, the mass, calculated logP and pKA values (see arrow 2). Also displayed is the InChI code, a link to the corresponding entry in the ChEMBL database and a link to the PubPharm structure search. 

Step 3: Exploration of interactions and associations. On the left side, you will see a navigation bar (see arrow 3) that will take you to the various extracted information in the Drug Overviews at any time.
An important note: All displayed associations were automatically extracted from the literature. Unfortunately, possible incorrect extractions cannot be excluded.

Drug-Target-Disease Networks

The Drug Overviews visualise extracted associations to other drugs, diseases and targets in a so-called Drug-Target-Disease Network (see arrow 4). Here, the respective concepts are represented as nodes and their associations as edges. The numbers on the edges indicate how many documents from the literature support the respective association. Clicking on an edge triggers a corresponding search in the Narrative Service for literature. If you click on a node in the network, the associations between the clicked node and the already existing network are displayed. If you want to hide diseases, e.g., you can do so in the upper left area of the networks.

Drug aspects

Further down in the Drug Overviews, various imformation of the active substances are compiled (see arrow 5). For example, the first box shows possible indications of the active substance. In our example, the first group is diabetes mellitus, which is supported by 4546 documents from the literature (see the small blue box). The Roman numeral "IV" indicates that the treatment of this disease with metformin is in clinical phase 4 (based on ClinicalTrials.gov). Clicking on the number will then direct you to the appropriate source: corresponding literature search in the Narrative Service or an entry in ClinicalTrials.gov. 

Other aspects include dosage forms (administration), interactions with targets, laboratory methods, species, human target groups ("HealthStatus"), drug associations and interactions, as well as adverse effects and effects on tissue.

There is a search bar in the upper right area of each box that you can use to filter in the box (e.g., "Diabetes"). You can also adjust the sorting in the individual boxes. Below the last box, the latest publications on the active substance are displayed.

 

Does it make a difference weather I search from the smartphone or from the desktop PC?

  • The web design of PubPharm is responsive. That means the website is displayed well on different devices - from smartphones to desktop PC.
  • No matter from which device you are searching, all tools and functions, e.g., the service Drug Overviews, filters, favourites lists and export functions, can be used. The only exception is the structure search.
  • Please note that the layout of the individual elements may differ on different devices. In the desktop view the info boxes are arranged horizontally, while in the smartphone view they are found in a vertical order.

Where can I get more information?

The PubPharm Blog, posts on Twitter/X and Mastodon, and the LinkedIn account provide information on current developments in FID Pharmazie. Information materials, including up-to-date handouts, flyers and video tutorials, can be accessed here. The PubPharm Quiz also offers the opportunity to test the PubPharm functionalities (with suggested solutions) on examples.
PubPharm and all other FID services are continuously developed and optimised. Questions, suggestions or other feedback are always welcome! You can reach the FID project team as follows:

  • By contact
  • By email: pubpharm [at] tu-braunschweig.de
  • By phone: +49531 391 5046 or -5003
  • By letter or in person: Fachinformationsdienst Pharmazie, Universitätsbibliothek Braunschweig, Universitätsplatz 1, 38106 Braunschweig