Access and run LaPsus

What is it ?

LaPsuS is a web interface based on Zope and written in Python. It helps users find scientific papers using advances searches on PubMed, a service mantained by the National Center for Biotechnology Information (NCBI) that includes more than 16 million bibliographic citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and preclinical sciences.

In LaPsuS, the user can enter up to three lists of biomedical terms. The lists are joined by logical operators (and, or, not). The software takes the terms and the operators, combines them to compose all the possible sentences and submits these sentences to the PubMed database. The interface offers different options: it is possible to search papers by authors and by journal, by date of publication and date of publication in PubMed. The user can search papers containing full text, free text or abstracts. A pull down menu allows the user to select the sorting method: by id (ascending or descending order), by title (in alphabetical order), by author (in alphabetical/reverse order), by journal (in alphabetical order), by publication date (from the older to the newer or vice versa).

The search action is divided in two steps: in the first step LaPsuS submits the sentences to the PubMed database using the "esearch" function. This function searches for publications containing the terms in each sentence and gives the respective numeric id. Each id is stored in a proper list. The second step is performed using the "efetch" function: this function uses the ids in the list to make the queries and gets, for each id, an XML document containing all the information about the publication related to the id. Then LaPsuS parses each XML document to extract the information the user has requested for (for example the title, the authors, the journal, the publication date and so on) and writes it in a Python dictionary. The keys of the dictionary are the ids of each publication, the values are the title, the authors, the journal, the publication date. These data are subsequently shown in a table inside an HTML page. Each row contains a checkbox to select the data for export to file. Each ID is linked to the corresponding PubMed entry. In LaPsuS available export formats are CSV, BibTeX, endNote and HTML document.