Quick search

The Quick Search interface is located on the home page for MarinLit. This search is designed to allow you to perform a limited set of searches and get results quickly. Using Quick Search you can search for articles or compounds by selecting the appropriate radio button.

Important: All quick searches in MarinLit will return exact matches only.

Articles

You can search MarinLit using any text identifier. A search will return any article that matches the search term in any of the following fields:

  1. Title
  2. Old or new MarinLit ID
  3. Journal name
  4. DOI
  5. Trivial name
  6. Categories

For example, the search term phakellin will return any articles where phakellin is mentioned in the title or is listed as a trivial name in that article.

Note that MarinLit IDs of the form Axxxxx will return records matching the new ID. MarinLit IDs of the form xxxxx will return records matching the old FoxPro ID.

Compounds

You can run a Quick Search of compounds listed in MarinLit by name, molecular formula and exact mass.

Name

The compound Quick Search is run on the common or trivial name of a compound. Please note that the search only returns exact matches.

Molecular formula

You can also choose to search MarinLit by molecular formula. To do this: Enter the molecular formula that you are interested in surrounded by square brackets ( [ ] ). For example, [C11H13N5O]. (Note: the order of the elements is not important, so [N5C11OH13], works just as well)

When performing a molecular formula search from the Quick Search interface the search will only return records that are an exact match. For more complex searches use the interface on the Compound search page.

Exact mass

The Quick Search interface also accepts searches on exact masses. You can choose to search for single value or search over an exact mass range.

Single exact mass – If you enter a single value; for example, 242.1280, then only an exact match will be returned.

Mass range – If you enter a range (separated with a hyphen), for example, 210.2-214.2, you will obtain a list of records that have an exact mass that falls between your boundary conditions.

Main searches

The main search pages are designed to allow you to search across a large variety of different types of data using text or numerical values.

MarinLit has three main searches available – Bibliographic, Compound and Taxonomy. These allow you to focus your search on the information that is most important to you. It is possible to combine all three searches, see the section Combined searches for more information.

Most of the search fields on a page have a Question Mark icon next to them, if you click on these then you will open a balloon containing some basic data on the types of input that it takes (and in some cases a link to further help).

Bibliographic search

This is the main search for article data in MarinLit. The Bibliographic Search allows a tailored search of many MarinLit data fields, including MarinLit ID, author name, citation data, categories and trivial names.

Important: When performing a search using multiple parameters, the individual queries are combined in an additive manner, which means that you will only obtain results where there are records that match all criteria:

For example, a search for Author family name: Smith, Category: Alkaloids will return results for Author family name: Smith AND Category: Alkaloids.

Please note that MarinLit ID must be entered as numbers only (with no leading A) and will only return new system IDs.

Categories (Keywords)

MarinLit uses 300 categories to describe features of each paper, such as geographical region, biological activity, structural class, experimental techniques and source organism. These are arranged in a hierarchical structure.

To add a category, click on the down arrow in the box. Any number of desired categories can be selected from the pop up menu using the tick boxes. Once the correct categories have been selected, click Apply.

Categories are divided into 19 groups covering similar terms. To perform a more general search, the top level category can be selected. This will return articles that match any of the keywords in that group.

For example, selecting Pharmacology will return results with any of the categories Chemotherapy, Pharmacokinetics and Pharmacological techniques.

To remove a selected category from the search, click the X next to the category in the search box.

To add an additional category, click in the category box and repeat the process.

Journal name

To add a journal name, select it from the drop down list. To see suggested journal names, begin typing in the box and matches will appear in the list below. Please note that MarinLit uses the CAS Source Index (CASSI) abbreviations for journal names.

To remove a selected journal name from the search, click the X next to the word in the search box.

To add an additional journal name, click in the journal name box and repeat the process.

Trivial name

To add a trivial name, select it from the drop down list. To see suggested trivial names, begin typing in the box and matches will appear in the list below. This search will return all articles that are related to a compound with that trivial name.

To remove a selected trivial name from the search, click the X next to the word in the search box.

To add an additional trivial name, click in the trivial name box and repeat the process.

Compound search

The compound search in MarinLit contains many powerful tools for dereplication of newly isolated compounds, including structure, NMR features and functional groups, molecular formula, exact mass, UV λmax and 13C NMR and 1H NMR predicted shifts.

In MarinLit, the compound search is divided into three tabs – Structure and properties, Functional groups and NMR chemical shifts. Data can be entered into all three tabs to produce a combined search on all the data.

Important: The data in the Structure and properties, Functional groups and NMR chemical shifts tabs are used to make an additive search. Results will only be returned for compounds that match all the criteria specified.

Structure and properties

Structure Search

The Structure Search page allows you to search MarinLit by chemical structure. This can be an exact structure search or you can perform Substructure or Similarity searches to allow you to find any structures related to your query structure.

When performing a Substructure or Similarity search it is possible to combine your structure search with queries from the Properties, Functional groups and NMR Chemical Shifts sections.

Structure Search interface

The Structure Search interface provides a box that displays the structure to be searched on together with buttons that allow you to modify or input a new structure(s). The Options menu allows you to perform Exact, Substructure and Similarity Searches (see subsections for more details)

Entering (and editing a new structure)

There are two buttons displayed in the Top-left corner of the Structure display box; Convert and Edit.

The Convert option can be used to input complex chemical structures quickly, based on conversion of a text identifier to a structure.

Clicking on the Convert button displays a prompt that will accept a SMILES string (Simplified Molecular-Input Line-Entry System ) or an InChI string (International Chemical Identifier). You can also input a systematic chemical name.

When you click on OK, the system will attempt to generate the structure that corresponds to your input. At this point you can perform a search on the structure as is, or use the Edit option to modify the structure.

The Edit option can be used to draw from scratch or modify a chemical structure. We have integrated two structure editor interfaces:

  • JSDraw (http://www.scilligence.com/Web/JSDraw.aspx will work on systems that do not run Java e.g. devices that use iOS )
  • JChemPaint (http://jchempaint.github.com/ in browsers that do not support HTML 5). Additionally, JChemPaint provides the ability to paste structures drawn in other editors directly into the editor and also the option to open a file that contains a structure (e.g. mol, sdf, rxn)

Clicking on the Edit button will open the structure editor interface in a pop-up. By default JSDraw is displayed, but you can easily change to JChemPaint by selecting the tab near the top of the pop-up.

Note: Only JChemPaint supports the ability to cut and paste structures in (and out) of the editor from external programs such as ChemDraw or ChemSketch.

Once you have entered your structure, click OK to close the structure Editor interface.

Structure Search Options

The Structure Search options work as follows:

Exact Search

  • Strict

When selecting this option the system will search for the molecule exactly as drawn including any stereochemistry or isotopic labelling that you have defined

  • All tautomers

This option is useful for searching when your input structure may be depicted in more than one tautomeric form, e.g. Ethyl malonate, which can be drawn as a keto-ester or an enol ester.

  • Allow isotopes and stereoisomers

This option is useful for performing a slightly more general search to see whether there are any related stereoisomers or isotopomers in MarinLit.

Note: An exact structure search cannot be combined with a properties search.

Substructure Search

The Substructure Search allows you to search MarinLit for molecules that contain the structural fragment that you have specified. Note: We do not currently support any special structural wildcards.

You can choose to restrict your search to the particular tautomer that you have drawn, or allow matching of any tautomeric structure (where relevant)

Important: When performing a Substructure Search it is advisable to choose a large, functionalised structure as a starting point and then simplify the query structure gradually to widen your results set.

Similarity Search

The Similarity Search option allows you to find compounds that are similar to (but do not necessarily match all of the features of) your specified structure. It is possibility to change the level of similarity that the results must have with your input structure (from >99% to >70%) as well as the method of determining the similarity: Tanimoto, Tversky or Euclidian.

Important: When performing a Similarity Search we would always advise you to start by specifying a high degree of similarity and then decrease the level of similarity incrementally as needed.

Text search

The text search allows inclusion of article data in the compound search, for example, compound name.

Compound name

This field accepts any name/synonym that might be used in MarinLit, e.g. trivial name or systematic name. This field only makes exact matches.

Compound status

Filter searches by only returning compounds with a certain status, for example, those that are new to the literature or are structural revisions of earlier structures.

Compounds reported in MarinLit can have a status from the following:

New – this is the first report of this compound in the literature

New to marine – this compound has been reported in the literature previously, but this is the first report from a marine source

Revision – the structure of this compound is a revision of an earlier structure for the same molecule

If the structure of a molecule has been revised in a later article, then the compound status of the original structure will change to one of the following, as appropriate:

New and revised in a subsequent article

New to marine and revised in a subsequent article

Revision and revised in a subsequent article

The default setting is All, where results with any compound status can be returned.

Free text

This field allows you to perform a free text search across all of the fields contained within the records.

Properties search

The properties search consists primarily of numeric searches across experimentally measured and calculated data. Many of the fields accept two inputs, a main value together with an input that allows you to specify the boundary conditions of the search.

Molecular formula

In contrast to the Quick Search interface, you do not need to use brackets in your query when you search using the Molecular Formula field in the Search page.

For example, C6H10 returns a number of results. When searching using this field, the query returns not only results that are an exact match i.e. has the molecular formula C6H10, but also results for compounds that contain C6H10, so you can also get matches for molecular formulae such as C6H10N, C6H10O, C6H10O2 etc.

It is also possible to specify that the molecular Formula Search covers a range of molecular formulae e.g. C10-12H22O2, will match C10H22O2, C11H22O2 and C12H22O2

UV maxima

Search by Absorption Max value, this field expects a wavelength that should be provided in nanometres (nm).

If you would like to search for compounds using more than one Absorption Max value, then click the button Add more values. Note that these values will be searched in an AND manner.

Exact mass

You can choose to search for an exact mass (boundary condition = 0) or over a range of exact masses, by specifying a value +/- variance.

Both the main value and boundary conditions fields allow you to enter values to an accuracy of 4 d.p.

Functional Groups search

The Functional Group search is designed to search compounds by features that are easily determined by 1H NMR and 13C NMR.

You can enter either the exact number of each type of functional group or a range of numbers (separated by a hyphen). To exclude a functional group, set the number of that group to 0.

It is not necessary to fill all the boxes. All empty boxes will be considered as unknown and results containing these functional groups will be returned.

Additional functional groups can be accessed by maximising and collapsing using the + and – buttons.

For example, if a compound of interest is known to contain 3 singlet methyl groups, 1 terminal alkyne and no benzene rings, place a 3 in the singlet methyl box, 1 in the terminal alkyne box and 0 in the total benzenes box.

Notes regarding the functional group search:

Total methyl groups includes methoxyl (O-methyl), N-methyl, S-methyl and acetyl groups.

Singlet, doublet and triplet methyl only refer to CH3–C type methyls.

Vinyl methyl does not include aromatic methyl groups.

Total C=C excludes benzene and pyridine ring double bonds.

Total C–O includes all alcohols, ethers (count as 2 C–O), esters and lactones (both count as 1 C–O). Single bonds from the sp2 carbon to oxygen in acids, esters and lactones are not included.

Total C=O includes ketones, aldehydes, amides, esters etc.

Acetyl includes acetate esters and amides.

Aldehyde includes formyl groups.

Imine does not include C=N bonds in pyridines.

NMR Chemical Shifts search

Calculated 13C and 1H chemical shift data are provided by Advanced Chemistry Development, Inc. (ACD/Labs) for all compounds. The data can be searched by inserting a chemical shift value and a variance (+/-). A default variance of 2 (for 13C) and 0.2 (for 1H) will be used if not changed by the user. A hit will be returned if the calculated shift value is within the range specified by the user.

For 13C data, it is also possible to specify the number of attached hydrogen atoms (0–3 or Any) for a carbon signal.

To add more NMR signals, click the Add more box at the bottom of the appropriate list. To delete one inserted shift from a list, click the to the right of the line to be deleted.

If both 13C and 1H shifts are provided, results will be returned that match all shifts listed.

Taxonomy search

The Taxonomy Search can search any of the taxonomy data in MarinLit. It is not necessary to complete a full taxonomy for a search.

To add a taxonomic name, select it from the drop down list. To see suggested taxonomic names, begin typing in the box and matches will appear in the list below.

To remove a selected taxonomic name from the search, click the X next to the word in the search box.

Once a taxonomic name has been selected in any box, the options available in all other levels of the taxonomy will be automatically restricted to those that correspond to the selection.

For example, if the genus Agelas is selected, the only available phylum is Porifera.

To only view articles where the organism of interest is a source of natural products, tick the Source of compound (*) box.

Searching more than one taxon

It is possible to search more than one set of taxonomic data as an OR search. Set the first taxonomy required as above, and click Add to search. Repeat for each subsequent taxonomy, adding each to the search. One all required taxonomy data is entered, click Search. Multiple taxa can be combined with other searches in the same way as a single taxon.

To edit taxonomy data that has been added to the search, click on the edit. This will populate the boxes above. Make the required changes and then click Update to change the search criteria.

To delete taxonomy data that has been added to the search, click on edit in the corresponding row.

Location search

The Location search allows users to search collection locations from which new compounds have been reported.

The search works by setting a central point, using any of the location name, coordinates or by placing a pin on the map, and entering a search radius around this point.

Searching by location name

Enter the location name in the Location name search box and select the correct location from the dropdown box or click Go. This will drop a pin on the map in the specified location.

Set the required search radius in miles and click Search at the bottom of the page.

Searching by coordinates

Enter the latitude and longitude coordinates in the boxes provided. Note that coordinates must be in decimal format (e.g. -45.2236, 10.2300; not 45° 13' 24.96" S, 10° 13' 48" E). Set the required radius in miles and click Search at the bottom of the page.

Searching by placing a pin

Navigate to the required location on the map and drop a pin using a single left click. Set the required radius in miles and click Search at the bottom of the page.

Location search results will be displayed as a list of compounds found within the specified search area. To view the results on a map, click the View on map button at the top of the results list.

Collection locations are displayed that fall within the search area. Pin colours reflect the precision of the location data given in the original article (green = exact/very precise, yellow = near, red = in the region of).

If two or more collection locations are close together, they are combined into a single blue circle. To zoom in on these locations, click on the blue circle .

To view compounds found at each location, click on the location pin. To navigate directly to the compound record, click on the compound name in the information bubble.

If more than five substances have been found at a location, click in the text at the top of the bubble to see the full list of search results.

Please note that location data is not complete for all collection sites, but will be included for all 2014 records and beyond listing a collection site.If a depth is not given for a collection site, it will not be returned if a depth is specified in a search

Combined search

It is possible to combine Bibliographic, Compound, Taxonomy and Location searches by navigating through each search page as required.

Simply begin the search in one search area (for example Taxonomy) and enter the criteria, e.g. Phylum: Porifera.

Then use the blue buttons on the top right to navigate to the next search area, e.g. Compound search.

The current search criteria will now appear at the top of the new search page.

The next set of criteria can then be entered using the new search page. Once this is complete, simply navigate to another search page to enter more criteria there.

To remove a search term, simply click the x next to the term in the box at the top of the page.

Once the combined query is complete, click Search on any search page to run a search on all listed criteria.

Note that for a Combined Search, Clear will only act on the search page that is currently active. To discard all search criteria, select Start a new search.

Viewing results

Whenever you perform a search a new page will be displayed, this results page will show the number of results that were obtained and the search parameters that you specified.

Depending on the search you have run, the results will either be a list of articles or a list of compounds matching the search parameters.

Article results

The article list can be filtered by journal, author or category by clicking on the appropriate name in the boxes on the right. Filters that have been applied can be seen in the boxes at the right of the results page. To remove a filter, click the x next to the filter name. Clicking Refine category will bring up the pop up list of all categories for selection.

Citations can be downloaded by selecting the required records and choosing the reference manager format required. Then press Go.

If an article in the results list contains compounds, they can be viewed by clicking on Show compounds on that record. This will open the compound records for that article in the results list.

Both the new MarinLit ID and the old MarinLit ID are visible on the record. The new ID takes the form Axxxx, while the old ID is displayed in brackets alongside it.

Article record

For further information on an article, click on the title. This will take you to the article record page, including full citation, trivial names, keywords, compound data, taxonomy and collection location visualised in Google Maps. Clicking on the DOI link will take you to that article on the publisher’s website.

To view the next/previous article in the search results list without returning to the results list, click the Next record >> or << Previous record link at the top of the record.

To return to the results list, click << Back to search results at the top of the record.

Switching between article and compound results

After performing an article search, it is possible to view all compounds reported in the result set by clicking Display compounds in the top right.

Compound results

By default, compound results are displayed in a list view, with structure, name, formula, exact mass, InChiKey, status and ID. To display a grid view of the structures, select the desired grid size from the options in the grey box at the top. To return to the list view, click the blue list button at the top of the results.

Compound record

To view further compound information, click on the compound name. This will take you to the compound record.

Full compound information is provided in the record. The InChi and InChiKey can be copied by clicking the icon next to the required text.

The BindingDB section indicates how many structures that compound is linked to in BindingDB (www.bindingdb.org). To view the BindingDB results, click on the number and you will be directed to the BindingDB website. Binding DB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be targets of small, drug-like molecules.

The Articles section of the record gives details of the article in which the compound with this structure was first reported (either as a new compound or a revision of an earlier structure).

The Tools section of the record uses the predicted data from ACD/Labs to give a calculated 13C NMR spectrum, calculated HSQC-DEPT spectrum and a list of the calculated CH shifts by clicking the relevant button.

The compound structure can be downloaded as a tif file, by clicking on the Image button, or as a mol file by clicking on the Structure button. The mol file can be opened with most cheminformatics programs, including NMR software such as ACD/Labs Predictor.

To view the next/previous compound in the search results list without returning to the results list, click the Next record >> or << Previous record link at the top of the record.

To return to the results list, click << Back to search results at the top of the record.

Switching between compound and article results

After performing a compound search, it is possible to view the articles associated with the compounds in the results set by clicking Display articles in the top right.

Modify search

To quickly remove search criteria, click the x next to the word at the top of the results page. The list of results will automatically update.

A search query can be modified by clicking the Change this query button at the top of the results list. This will return you to a search screen with all the current criteria filled in.

To begin a new search, click Start a new search at the top of the results list and select the type of search required.

Further questions

Any further questions or comments can be directed to the MarinLit team. We welcome your feedback.

© Royal Society of Chemistry