Health informatics lecture 5

What concerns the acquisition, organization, and searching of knowledge based information, sometimes called a search?

Information retrieval (IR)

What is information derived and organized form observational or experimental research?

Knowledge based information

What did traditional biomedicine concentrate on during information retrieval?

Text from biomedical literature

What has information retrieval in the study of biomedicine become more recently or grown to include?

Now it includes images, video, chemical structures, gene and protein sequences, and wide range of other digital media of relevance to biomedical education, research, and patient care

What is the goal of the information retrieval process?

TO find content that meets a person’s information needs

What are the four components of information retrieval systems? Which one do the other three connect to?

Queries, metadata, content, search engine. All of them connect to metadata

What does a search engine do?

It queries the metadata databases and retrieves results related to the search query

What is metadata?

Data about data (tags, classes)

How is metadata created?

By indexing the content, the process is indexing

What kind of information does information retrieval focus on?

Knowledge based information

What are the two categories of knowledge-based information

Primary knowledge and secondary knowledge

What type of knowledge-based information is information that is original research that appears in journals, books, reports, and other sources? The kind of knowledge that was not known before, novel.

Primary knowledge

What kind of knowledge-based information is based on information that consists of the writing that reviews, condenses, and or synthesized the primary literature?

Secondary Knowledge

What is the most common example of secondary knowledge of literature?

Books, monographs, and review articles in journals and other publications

Would a series of the first research articles on covid 19 be primary or secondary knowledge?

Primary

Would a summary of all the resources and literature available for a certain topic be primary or secondary knowledge?

Secondary

Secondary knowledge must ____ the primary knowledge it used

CITE the primary knowledge it used

What is the use of secondary knowledge if it is just restating existing knowledge?

Instead of reading 1000 articles about a topic, you can read one and get a good idea about the field of that topic, then you can focus on specific branches

Where are virtually all scientific journals published?

They are all published electronically

What are three benefits of publishing articles electronically?

1. Articles have higher chance to be cited by other papers

2. convenient access and more available to public

3. Spreads knowledge faster

What two tasks do electronic articles eliminate from publishers?

Printing and mailing

What value do publishers still add to electronic articles even though they don’t print or mail them anymore? What is their new job?

They still hire and manage editorial staff and manage the peer review process

How were articles published in the past? Or rather what form where they published in?

Research articles were closed access published where only large organizations that paid a subscription could access the publishers articles

What is the new principle of open access publishing?

Anyone can go on the internet and access the article

Who pays the cost of publishing with open access articles?

The author or their institution pay the cost up front and then allow their articles to be free online

Where do authors get the money for open access publishing?

Since most research is funded by grants, the cost of publishing is usually included in the

What is the main benefit of open access publishing?

The quick dissemination of knowledge

What is one disadvantage of open access publishing

Since authors pay the fees, the publisher will publish anything to get more money, even if its not accurate or of good quality

What kind of information includes the reference to a single, specific article and can be found for virtually any article?

Bibliographic information

What is included in bibliographic information

Authors, title of paper, scientific journal, year and month of publication, volume, issue

Where is bibliographic information organized? What is the a well known example of this?

Bibliographic information is stored in databases where you can be taken to the full text by following the hyperlinked reference. A good example is Medline. NOTE: does not contain the actual articles, just references to them

What category of information content is the actual written text of the literature (books, articles, journals, etc) and is mostly online

Full text content

What kind of information content is edited or analyzed based on existing content and is then stored into a database? Usually takes data and helps turn it into information

Annotated content

What would be an example of annotated information content?

A gene sequence that has been annotated for known gene sequences, domains, coding regions, etc.

What kind of information is a specialized collection for a specific topic

Aggregated content

What is the process of assigning metadata to content?

IndexingWha

What is the purpose of indexing?

Faciliating retrieval

What are the four categories of information content?

Bibliographic, full text, annotated, aggregated

What kind of indexing is where human indexers using a controlled terminology, assign indexing terms and attributes to a document, usually following a protocol? Does take a while

Manual indexing

What kind of indexing uses computers to making indexing assignments by breaking out each work in the document as an indexing term?

Automated indexing

What kind of data becomes metadata?

Authors, affiliated intuitions of authors, year, volume, issue, title of paper, DOI (digital object indentifier) link, (Notice this is all bibliographic information) then a list of keywords on what the article is about

What contains a set of terms that can be applied to a task, such as indexing?

A controlled terminology

What is a terminology that defines the terms called?

A vocabulary

What is a terminology that contains variants or synonyms of a terms called?

A thesaurus

With a thesaurus type terminology, what kind of relationships can there be between the terms?

Hierarchical, synonym, and related terms

What type of thesaurus relationship includes terms that are narrower or broader?

Hierarchical

What kind of thesaurus relationship includes different words with the same meaning?

Synonyms

What kind of thesaurus relationship includes terms that are no synonymous or hierarchical but are somehow related?

Related (hypertension is related to syphgmometer)

What kind of relationship exists between MeSH trees?

Hierarchical terms

What does MeSH stand for?

Medical subject heading

What is MeSH used for?

Manually indexing most databases produced by NLM

How many terms does the latest version of MeSH contain?

26,000 terms

How many of the thesaurus relationships does MeSH include?

All three relationships (hierarchical, synonyms, and related)

How many hierarchical trees does MeSH have?

16 subject trees (diseases, organisms, chemical and drugs) that branch off into specific from the roots

What is this image an example of?

A MeSH hierarchical tree

What type of indexing is most commonly done for bibliographic and annotated content but can be done for other forms of information?

Manual indexing

What is the golden standard and more trusted form of indexing?

Manual indexing is more trusted

Is most web content indexed automatically or manually?

Automatically

What does DCMI stand for?

Dublin Core Metadata Initiative

What is the goal of the DCMI?

Develop a set of standard data elements that creators of web resources can use to apply metadata to their content

Why would web creators want to properly index their content?

They want to be found easily, otherwise no one will find it

DCMI has been approved by who?

National information standards organization and the international organization of standards specification

What elements have been defined by DCMI?

Title, creator, subject, description, publisher, and date

Automated indexing is done by computers and is far faster than manual indexing, but how does it do it?

It indexes the document by defining all the words in the article and pulling the important ones that match existing keywords

What formula defines the weight of a term or how important it is?

The TF*IDF weighting

What is the formula for TF*IDF auto indexing?

Then you just multiply the two terms as the name suggests

What are some limitations of automated indexing

• Synonymy leads to underrepresentation of a term because it cannot count the synonyms

• Polysemy, same word, different meaning, inaccurate indexing

• Content, mentions of other related conditions could skew the actual topic of the article

• Context, words take different meaning based on the words around them

• Morphology, suffixes that don’t change the meaning but are unrecognizable to computers

• Granularity, describing content at different levels of hierarchy, putting a general article in a specific branch or vice versa

What is the retrieval system at NLM that searches Medline and other bibliographic databases?

Pubmed

What is an organized array of information?

A database

What is the purpose of a database?

To put information into it and be able to get them out again easily

How do databases simplify the information space?

By specializing/categorizing the information

Using an example, pretend this is a library, what would each element of this hierarchy look like in a library?

Data=books

Storage system=bookshelves

Query system=numbering system, labeled books, specific shelves

Information system=library

What is an indexed collection of information called?

A database

What are the three main terms that make a database?

• Entry, every record stored in the database

• Field, each entry consists of multiple fields that form the column heads

• Value, each field has a value that makes up the actual data

What type of database is made up of a long text file in which entries are separated by a special character, fields are separated by commas or tabs? What is the issue with this form?

Flat file database and the issue is the whole file must be searched to find a particular piece of data

What type of database stores data within a number of tables, each with tables and fields

Relational database

Do the tables in a relational database have the same different fields and records? How do they work?

Each table has different fields and records but are linked to at least one other table by a shared field called the key

The keys in a relational database must be __________

Unique

What are the benefits of relational databases?

Data is organized much more logically and can be searched much quicker.

What kind of database stores data as objects?

Object oriented databases

What is a unit that combines dtaa and mathematical routines that can act on the data?

Objects in object oriented databases

What links objects by defining relationships between them?

Pointers

What does object oriented databases allow data to be structured by?

complex hierarchical relationships in contrast to relational DB, very powerful, but lacks the rigirous logic of relational DB

What are the three main attributes of a database?

1. 1. Searchable (indexing)

2. 2. Updated periodically (release)

3. 3, Cross referenced (hyperlinked with other databases)